Fixed sorting on the show trait page

Added/improved the x and y axis on the bar graph and histogram

GEMMA working but still really slow

5 files changed, 110 insertions, 16 deletions

diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 6c1e65e9..98f89ac6 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -41,13 +41,15 @@ class Histogram
 

     create_x_scale: () ->

         console.log("min/max:", d3.min(@sample_vals) + "," + d3.max(@sample_vals))

-        if (d3.min(@sample_vals) < 0)

-            min_domain = d3.min(@sample_vals)

-        else

-            min_domain = 0

+        x0 = Math.max(-d3.min(@sample_vals), d3.max(@sample_vals))

+        #if (d3.min(@sample_vals) < 0)

+        #    min_domain = d3.min(@sample_vals)

+        #else

+        #    min_domain = 0

         @x_scale = d3.scale.linear()

-            .domain([min_domain, parseFloat(d3.max(@sample_vals))])

-            .range([0, @plot_width]) 

+            .domain([d3.min(@sample_vals), d3.max(@sample_vals)])

+            .range([0, @plot_width])

+            .nice()

 

     get_histogram_data: () ->

         console.log("sample_vals:", @sample_vals)

@@ -62,6 +64,7 @@ class Histogram
 

     create_graph: () ->

         @add_x_axis()

+        @add_y_axis()

         @add_bars()

 

     add_x_axis: () ->

@@ -74,11 +77,32 @@ class Histogram
             .attr("transform", "translate(0," + @plot_height + ")")

             .call(x_axis)

             

+    #add_y_axis: () ->

+    #    y_axis = d3.svg.axis()

+    #            .scale(@y_scale)

+    #            .orient("left")

+    #            .ticks(5)

+    #            

+    #    @svg.append("g")

+    #        .attr("class", "y axis")

+    #        #.attr("transform", "translate(0," + @plot_width + ")")

+    #        .call(y_axis)

+            

+            

     add_y_axis: () ->

-        y_axis = d3.svg.axis()

+        yAxis = d3.svg.axis()

                 .scale(@y_scale)

                 .orient("left")

                 .ticks(5)

+

+        @svg.append("g")

+            .attr("class", "y axis")

+            .call(yAxis)

+          .append("text")

+            .attr("transform", "rotate(-90)")

+            .attr("y", 6)

+            .attr("dy", ".71em")

+            .style("text-anchor", "end")

                 

     add_bars: () ->

         console.log("bar_width:", @x_scale(@histogram_data[0].dx))

diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 1603cb77..d8067ced 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -55,14 +55,10 @@
     };
 
     Histogram.prototype.create_x_scale = function() {
-      var min_domain;
+      var x0;
       console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
-      if (d3.min(this.sample_vals) < 0) {
-        min_domain = d3.min(this.sample_vals);
-      } else {
-        min_domain = 0;
-      }
-      return this.x_scale = d3.scale.linear().domain([min_domain, parseFloat(d3.max(this.sample_vals))]).range([0, this.plot_width]);
+      x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
+      return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
     };
 
     Histogram.prototype.get_histogram_data = function() {
@@ -82,6 +78,7 @@
 
     Histogram.prototype.create_graph = function() {
       this.add_x_axis();
+      this.add_y_axis();
       return this.add_bars();
     };
 
@@ -92,8 +89,9 @@
     };
 
     Histogram.prototype.add_y_axis = function() {
-      var y_axis;
-      return y_axis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+      var yAxis;
+      yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+      return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
     };
 
     Histogram.prototype.add_bars = function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 84e465e8..a410baf3 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -204,6 +204,7 @@ $ ->
                 name = $.trim(name)
                 real_value = $(row).find('.edit_sample_value').val()
                 console.log("real_value:", real_value)
+                
                 checkbox = $(row).find(".edit_sample_checkbox")
                 checked = $(checkbox).attr('checked')
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index f1024cd1..1d375686 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -56,6 +56,9 @@ $ ->
         console.log("In interval mapping")
         $("#progress_bar_container").modal()
         url = "/interval_mapping"
+        $('input[name=method]').val("reaper")
+        $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'))
+        $('input[name=suggestive]').val($('input[name=suggestive_reaper]'))
         form_data = $('#trait_data_form').serialize()
         console.log("form_data is:", form_data)
         $.ajax(
@@ -116,9 +119,41 @@ $ ->
         return false
     )
 
+    $("#plink_compute").click(() =>
+        url = "/marker_regression"
+        $('input[name=method]').val("plink")
+        $('input[name=mapping_display_all]').val($('input[name=display_all_plink]'))
+        $('input[name=suggestive]').val($('input[name=suggestive_plink]'))
+        $('input[name=maf]').val($('input[name=maf_plink]'))
+        form_data = $('#trait_data_form').serialize()
+        console.log("form_data is:", form_data)
+        $.ajax(
+            type: "POST"
+            url: url
+            data: form_data
+            error: (xhr, ajaxOptions, thrownError) =>
+                alert("Sorry, an error occurred")
+                console.log(xhr)
+                clearInterval(this.my_timer)
+                $('#progress_bar_container').modal('hide')
+                $("body").html("We got an error.")        
+            success: (data) =>
+                clearInterval(this.my_timer)
+                $('#progress_bar_container').modal('hide')
+                $("body").html(data)
+        )
+        console.log("settingInterval")
+
+        this.my_timer = setInterval(get_progress, 1000)
+        return false
+    )
+
     $("#gemma_compute").click(() =>
         url = "/marker_regression"
         $('input[name=method]').val("gemma")
+        $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]'))
+        $('input[name=suggestive]').val($('input[name=suggestive_gemma]'))
+        $('input[name=maf]').val($('input[name=maf_gemma]'))
         form_data = $('#trait_data_form').serialize()
         console.log("form_data is:", form_data)
         $.ajax(
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index a5a49ace..dbc26e3b 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -67,6 +67,9 @@
       console.log("In interval mapping");
       $("#progress_bar_container").modal();
       url = "/interval_mapping";
+      $('input[name=method]').val("reaper");
+      $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
       $.ajax({
@@ -127,10 +130,43 @@
       _this.my_timer = setInterval(get_progress, 1000);
       return false;
     });
+    $("#plink_compute").click(function() {
+      var form_data, url;
+      url = "/marker_regression";
+      $('input[name=method]').val("plink");
+      $('input[name=mapping_display_all]').val($('input[name=display_all_plink]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_plink]'));
+      $('input[name=maf]').val($('input[name=maf_plink]'));
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      $.ajax({
+        type: "POST",
+        url: url,
+        data: form_data,
+        error: function(xhr, ajaxOptions, thrownError) {
+          alert("Sorry, an error occurred");
+          console.log(xhr);
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          return $("body").html("We got an error.");
+        },
+        success: function(data) {
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          return $("body").html(data);
+        }
+      });
+      console.log("settingInterval");
+      _this.my_timer = setInterval(get_progress, 1000);
+      return false;
+    });
     $("#gemma_compute").click(function() {
       var form_data, url;
       url = "/marker_regression";
       $('input[name=method]').val("gemma");
+      $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_gemma]'));
+      $('input[name=maf]').val($('input[name=maf_gemma]'));
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
       $.ajax({