Add show & hide BD buttons to single chr view

4 files changed, 33 insertions, 61 deletions

diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
index e00694be..d3c1ee7d 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.coffee
@@ -273,6 +273,7 @@ class Chr_Lod_Chart
         $("#return_to_full_view").hide()

         $('#topchart').remove()

         $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>')

+        hideBDButton()

         create_lod_chart()

 

     show_marker_in_table: (marker_info) ->

diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
index c6cbd01b..0032858f 100644
--- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js
@@ -1,13 +1,12 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.10.0
 var Chr_Lod_Chart;
 
 Chr_Lod_Chart = (function() {
-  function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) {
+  function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot) {
     this.plot_height = plot_height;
     this.plot_width = plot_width;
     this.chr = chr;
     this.manhattanPlot = manhattanPlot;
-    this.mappingScale = mappingScale;
     this.qtl_results = js_data.qtl_results;
     console.log("qtl_results are:", this.qtl_results);
     console.log("chr is:", this.chr);
@@ -66,6 +65,8 @@ Chr_Lod_Chart = (function() {
       } else {
         this_chr = result.chr;
       }
+      console.log("this_chr is:", this_chr);
+      console.log("@chr[0] is:", parseInt(this.chr[0]));
       if (this_chr > parseInt(this.chr[0])) {
         break;
       }
@@ -95,18 +96,11 @@ Chr_Lod_Chart = (function() {
   Chr_Lod_Chart.prototype.create_coordinates = function() {
     var i, len, ref, result, results;
     ref = this.these_results;
-    console.log("THESE_RESULTS:", ref)
     results = [];
     for (i = 0, len = ref.length; i < len; i++) {
       result = ref[i];
       this.x_coords.push(parseFloat(result.Mb));
-      if (js_data.result_score_type == "LOD") {
-        this.y_coords.push(result.lod_score);
-      }
-      else {
-        console.log("LRS VALUE:", result['lrs_value'])
-        this.y_coords.push(result['lrs_value']);
-      }
+      this.y_coords.push(result.lod_score);
       results.push(this.marker_names.push(result.name));
     }
     return results;
@@ -119,19 +113,7 @@ Chr_Lod_Chart = (function() {
   };
 
   Chr_Lod_Chart.prototype.create_scales = function() {
-    if (this.mappingScale == "morgan") {
-        max_pos = 0
-        for (i = 0, len = this.these_results.length; i < len; i++) {
-           marker = this.these_results[i]
-           if (parseFloat(marker['Mb']) > max_pos){
-               max_pos = parseFloat(marker.Mb)
-           }
-        }
-        this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]);
-    }
-    else {
-        this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
-    }
+    this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]);
     return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
   };
 
@@ -278,6 +260,7 @@ Chr_Lod_Chart = (function() {
     $("#return_to_full_view").hide();
     $('#topchart').remove();
     $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
+    hideBDButton();
     return create_lod_chart();
   };
 
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.coffee b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
index 55ffdce0..2da2e5bb 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.coffee
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.coffee
@@ -123,6 +123,8 @@ lodchart = () ->
                    .on("click", (d) ->
                       console.log("d is:", d)
                       redraw_plot(d)
+                      setBDData(d[0], d[1])
+                      showBDButton()
                     )   
   
         # x-axis labels
diff --git a/wqflask/wqflask/static/new/javascript/lod_chart.js b/wqflask/wqflask/static/new/javascript/lod_chart.js
index 014bf59b..c6d1045c 100644
--- a/wqflask/wqflask/static/new/javascript/lod_chart.js
+++ b/wqflask/wqflask/static/new/javascript/lod_chart.js
@@ -1,8 +1,8 @@
-// Generated by CoffeeScript 1.9.2
+// Generated by CoffeeScript 1.10.0
 var lodchart;
 
 lodchart = function() {
-  var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
+  var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks;
   width = 800;
   height = 500;
   margin = {
@@ -20,6 +20,7 @@ lodchart = function() {
   };
   titlepos = 20;
   manhattanPlot = false;
+  additive = false;
   ylim = null;
   additive_ylim = null;
   nyticks = 5;
@@ -29,8 +30,7 @@ lodchart = function() {
   darkrect = "#F1F1F9";
   lightrect = "#FBFBFF";
   lodlinecolor = "darkslateblue";
-  additivelinecolor_plus = "red";
-  additivelinecolor_negative = "green";
+  additivelinecolor = "red";
   linewidth = 2;
   suggestivecolor = "gainsboro";
   significantcolor = "#EBC7C7";
@@ -70,15 +70,14 @@ lodchart = function() {
         return results;
       })();
       ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])];
-
-      if ('additive' in data) {
+      if (additive) {
         data['additive'] = (function() {
           var j, len, ref, results;
           ref = data['additive'];
           results = [];
           for (j = 0, len = ref.length; j < len; j++) {
             x = ref[j];
-            results.push(x);
+            results.push(Math.abs(x));
           }
           return results;
         })();
@@ -92,12 +91,12 @@ lodchart = function() {
       g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none");
       yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]);
       yticks = yticks != null ? yticks : yscale.ticks(nyticks);
-      if ('additive' in data) {
+      if (additive) {
         additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]);
         additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks);
       }
       reorgLodData(data, lodvarname);
-      data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale);
+      data = chrscales(data, width, chrGap, margin.left, pad4heatmap);
       xscale = data.xscale;
       chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) {
         return "chrrect" + d[0];
@@ -118,7 +117,9 @@ lodchart = function() {
         return lightrect;
       }).attr("stroke", "none").on("click", function(d) {
         console.log("d is:", d);
-        return redraw_plot(d);
+        redraw_plot(d);
+        setBDData(d[0], d[1]);
+        return showBDButton();
       });
       xaxis = g.append("g").attr("class", "x axis");
       xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) {
@@ -133,7 +134,7 @@ lodchart = function() {
         var chr_plot;
         $('#topchart').remove();
         $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>');
-        return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale);
+        return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot);
       };
       rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1;
       yaxis = g.append("g").attr("class", "y axis");
@@ -148,7 +149,7 @@ lodchart = function() {
         return formatAxis(yticks)(d);
       });
       yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue");
-      if ('additive' in data) {
+      if (additive) {
         rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1;
         additive_yaxis = g.append("g").attr("class", "y axis");
         additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) {
@@ -187,19 +188,13 @@ lodchart = function() {
             return yscale(data.lodByChr[chr][i][lodcolumn]);
           });
         };
-        if ('additive' in data) {
+        if (additive) {
           additivecurve = function(chr, lodcolumn) {
-            if (data.additiveByChr[chr][0] < 0) {
-              pos_neg = "negative"
-            }
-            else {
-              pos_neg = "positive"
-            }
-            return [pos_neg, d3.svg.line().x(function(d) {
+            return d3.svg.line().x(function(d) {
               return xscale[chr](d);
             }).y(function(d, i) {
-              return additive_yscale(Math.abs(data.additiveByChr[chr][i]));
-            })];
+              return additive_yscale(data.additiveByChr[chr][i][lodcolumn]);
+            });
           };
         }
         curves = g.append("g").attr("id", "curves");
@@ -210,17 +205,12 @@ lodchart = function() {
             curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none");
           }
         }
-        if ('additive' in data) {
+        if (additive) {
           ref1 = data.chrnames;
           for (k = 0, len1 = ref1.length; k < len1; k++) {
             chr = ref1[k];
             if (chr.indexOf(data['chr'])) {
-              if (additivecurve(chr[0], lodvarnum)[0] == "negative") {
-                curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
-              }
-              else {
-                curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
-              }
+              curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)).attr("stroke", additivelinecolor).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none");
             }
           }
         }
@@ -305,13 +295,6 @@ lodchart = function() {
     manhattanPlot = value;
     return chart;
   };
-  chart.mappingScale = function(value) {
-    if (!arguments.length) {
-      return mappingScale;
-    }
-    mappingScale = value;
-    return chart;
-  };
   chart.ylim = function(value) {
     if (!arguments.length) {
       return ylim;
@@ -449,6 +432,9 @@ lodchart = function() {
   chart.yscale = function() {
     return yscale;
   };
+  chart.additive = function() {
+    return additive;
+  };
   chart.additive_yscale = function() {
     return additive_yscale;
   };
@@ -470,4 +456,4 @@ lodchart = function() {
     return chrSelect;
   };
   return chart;
-};
\ No newline at end of file
+};