Merge /home/lei/gene

5 files changed, 156 insertions, 112 deletions

diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 524e8d89..eef1cdc0 100755
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -29,7 +29,7 @@ class CorrScatterPlot(object):
         try:
             circle_color = params['circle_color']
         except:
-            circle_color = 'steelblue'
+            circle_color = '#3D85C6'
         self.circle_color = circle_color
         
         try:
@@ -41,7 +41,7 @@ class CorrScatterPlot(object):
         try:
             line_color = params['line_color']
         except:
-            line_color = 'red'
+            line_color = '#FF0000'
         self.line_color = line_color
         
         try:
diff --git a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee
new file mode 100644
index 00000000..29a0e8f7
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee
@@ -0,0 +1,67 @@
+root = exports ? this
+
+class Scatter_Plot
+    constructor: () ->
+        data = new Array()
+        samples_1 = js_data.samples_1
+        samples_2 = js_data.samples_2
+        i = 0
+        for samplename of samples_1
+            sample1 = samples_1[samplename]
+            sample2 = samples_2[samplename]
+            data[i++] = [sample1.value, sample2.value]
+        margin =
+            top: 100
+            right: 15
+            bottom: 60
+            left: 60
+
+        width = js_data.width - margin.left - margin.right
+        height = js_data.height - margin.top - margin.bottom
+        minx = d3.min(data, (d) ->
+            d[0]
+        ) * 0.95
+        maxx = d3.max(data, (d) ->
+            d[0]
+        ) * 1.05
+        miny = d3.min(data, (d) ->
+            d[1]
+        ) * 0.95
+        maxy = d3.max(data, (d) ->
+            d[1]
+        ) * 1.05
+        x = d3.scale.linear().domain([minx, maxx]).range([0, width])
+        y = d3.scale.linear().domain([miny, maxy]).range([height, 0])
+        chart = d3.select("#scatter_plot").append("svg:svg").attr("width", width + margin.right + margin.left).attr("height", height + margin.top + margin.bottom).attr("class", "chart")
+        main = chart.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")").attr("width", width).attr("height", height).attr("class", "main")
+
+        # draw the x axis
+        xAxis = d3.svg.axis().scale(x).orient("bottom")
+        main.append("g").attr("transform", "translate(0," + height + ")").attr("class", "main axis date").call xAxis
+
+        # draw the y axis
+        yAxis = d3.svg.axis().scale(y).orient("left")
+        main.append("g").attr("transform", "translate(0,0)").attr("class", "main axis date").call yAxis
+        g = main.append("svg:g")
+        g.selectAll("scatter-dots").data(data).enter().append("svg:circle").attr("cx", (d) ->
+          x d[0]
+        ).attr("cy", (d) ->
+          y d[1]
+        ).attr("fill", js_data.circle_color).attr "r", js_data.circle_radius
+        main.append("line").attr("x1", x(minx)).attr("y1", y(js_data.slope * minx + js_data.intercept)).attr("x2", x(maxx * 0.995)).attr("y2", y(js_data.slope * maxx * 0.995 + js_data.intercept)).style("stroke", js_data.line_color).style "stroke-width", js_data.line_width
+        chart.append("text").attr("x", width / 2).attr("y", margin.top / 2 - 25).text "Sample Correlation Scatterplot"
+        text = ""
+        text += "N=" + js_data.num_overlap
+        chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 - 5).text text
+        text = ""
+        text += "r=" + js_data.r_value + "\t"
+        text += "p(r)=" + js_data.p_value
+        chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 15).text text
+        text = ""
+        text += "slope=" + js_data.slope + "\t"
+        text += "intercept=" + js_data.intercept
+        chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 35).text text
+        chart.append("text").attr("x", width / 2).attr("y", height + margin.top + 35).text js_data.trait_1
+        chart.append("text").attr("x", 20).attr("y", height / 2 + margin.top + 30).attr("transform", "rotate(-90 20," + (height / 2 + margin.top + 30) + ")").text js_data.trait_2
+
+root.Scatter_Plot = Scatter_Plot
diff --git a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js
index 26132492..df1e62b6 100755
--- a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js
+++ b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js
@@ -1,115 +1,77 @@
-var data = new Array();
-samples_1 = js_data.samples_1;
-samples_2 = js_data.samples_2;
-i = 0;
-for (var samplename in samples_1){
-	sample1 = samples_1[samplename];
-	sample2 = samples_2[samplename];
-	data[i++] = [sample1.value, sample2.value];
-}
-   
-    var margin = {top: 100, right: 15, bottom: 60, left: 60};
-    var width = js_data.width - margin.left - margin.right;
-    var height = js_data.height - margin.top - margin.bottom;
-      
-    minx = d3.min(data, function(d){return d[0];})*0.95;
-    maxx = d3.max(data, function(d){return d[0];})*1.05;
-    miny = d3.min(data, function(d){return d[1];})*0.95;
-    maxy = d3.max(data, function(d){return d[1];})*1.05;
-    
-    var x = d3.scale.linear()
-              .domain([minx, maxx])
-              .range([0, width]);
-    
-    var y = d3.scale.linear()
-    	      .domain([miny, maxy])
-    	      .range([height, 0]);
- 
-    var chart = d3.select('#scatter_plot')
-	.append('svg:svg')
-	.attr('width', width + margin.right + margin.left)
-	.attr('height', height + margin.top + margin.bottom)
-	.attr('class', 'chart')
+// Generated by CoffeeScript 1.6.1
+(function() {
+  var Scatter_Plot, root;
 
-    var main = chart.append('g')
-	.attr('transform', 'translate(' + margin.left + ',' + margin.top + ')')
-	.attr('width', width)
-	.attr('height', height)
-	.attr('class', 'main')   
-        
-    // draw the x axis
-    var xAxis = d3.svg.axis()
-	.scale(x)
-	.orient('bottom');
+  root = typeof exports !== "undefined" && exports !== null ? exports : this;
 
-    main.append('g')
-	.attr('transform', 'translate(0,' + height + ')')
-	.attr('class', 'main axis date')
-	.call(xAxis);
+  Scatter_Plot = (function() {
 
-    // draw the y axis
-    var yAxis = d3.svg.axis()
-	.scale(y)
-	.orient('left');
+    function Scatter_Plot() {
+      var chart, data, g, height, i, main, margin, maxx, maxy, minx, miny, sample1, sample2, samplename, samples_1, samples_2, text, width, x, xAxis, y, yAxis;
+      data = new Array();
+      samples_1 = js_data.samples_1;
+      samples_2 = js_data.samples_2;
+      i = 0;
+      for (samplename in samples_1) {
+        sample1 = samples_1[samplename];
+        sample2 = samples_2[samplename];
+        data[i++] = [sample1.value, sample2.value];
+      }
+      margin = {
+        top: 100,
+        right: 15,
+        bottom: 60,
+        left: 60
+      };
+      width = js_data.width - margin.left - margin.right;
+      height = js_data.height - margin.top - margin.bottom;
+      minx = d3.min(data, function(d) {
+        return d[0];
+      }) * 0.95;
+      maxx = d3.max(data, function(d) {
+        return d[0];
+      }) * 1.05;
+      miny = d3.min(data, function(d) {
+        return d[1];
+      }) * 0.95;
+      maxy = d3.max(data, function(d) {
+        return d[1];
+      }) * 1.05;
+      x = d3.scale.linear().domain([minx, maxx]).range([0, width]);
+      y = d3.scale.linear().domain([miny, maxy]).range([height, 0]);
+      chart = d3.select("#scatter_plot").append("svg:svg").attr("width", width + margin.right + margin.left).attr("height", height + margin.top + margin.bottom).attr("class", "chart");
+      main = chart.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")").attr("width", width).attr("height", height).attr("class", "main");
+      xAxis = d3.svg.axis().scale(x).orient("bottom");
+      main.append("g").attr("transform", "translate(0," + height + ")").attr("class", "main axis date").call(xAxis);
+      yAxis = d3.svg.axis().scale(y).orient("left");
+      main.append("g").attr("transform", "translate(0,0)").attr("class", "main axis date").call(yAxis);
+      g = main.append("svg:g");
+      g.selectAll("scatter-dots").data(data).enter().append("svg:circle").attr("cx", function(d) {
+        return x(d[0]);
+      }).attr("cy", function(d) {
+        return y(d[1]);
+      }).attr("fill", js_data.circle_color).attr("r", js_data.circle_radius);
+      main.append("line").attr("x1", x(minx)).attr("y1", y(js_data.slope * minx + js_data.intercept)).attr("x2", x(maxx * 0.995)).attr("y2", y(js_data.slope * maxx * 0.995 + js_data.intercept)).style("stroke", js_data.line_color).style("stroke-width", js_data.line_width);
+      chart.append("text").attr("x", width / 2).attr("y", margin.top / 2 - 25).text("Sample Correlation Scatterplot");
+      text = "";
+      text += "N=" + js_data.num_overlap;
+      chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 - 5).text(text);
+      text = "";
+      text += "r=" + js_data.r_value + "\t";
+      text += "p(r)=" + js_data.p_value;
+      chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 15).text(text);
+      text = "";
+      text += "slope=" + js_data.slope + "\t";
+      text += "intercept=" + js_data.intercept;
+      chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 35).text(text);
+      chart.append("text").attr("x", width / 2).attr("y", height + margin.top + 35).text(js_data.trait_1);
+      chart.append("text").attr("x", 20).attr("y", height / 2 + margin.top + 30).attr("transform", "rotate(-90 20," + (height / 2 + margin.top + 30) + ")").text(js_data.trait_2);
+    }
 
-    main.append('g')
-	.attr('transform', 'translate(0,0)')
-	.attr('class', 'main axis date')
-	.call(yAxis);
+    return Scatter_Plot;
 
-    var g = main.append("svg:g"); 
-	
-    g.selectAll("scatter-dots")
-      .data(data)
-      .enter().append("svg:circle")
-          .attr("cx", function (d) { return x(d[0]); } )
-          .attr("cy", function (d) { return y(d[1]); } )
-		  .attr("fill", js_data.circle_color)
-          .attr("r", js_data.circle_radius);
-          
-    main.append('line')
-        .attr('x1', x(minx))
-        .attr('y1', y(js_data.slope*minx+js_data.intercept))
-        .attr('x2', x(maxx*0.995))
-        .attr('y2', y(js_data.slope*maxx*0.995+js_data.intercept))
-        .style('stroke', js_data.line_color)
-        .style('stroke-width', js_data.line_width);
-        
-    chart.append("text")
-      .attr("x", width/2)
-      .attr("y", margin.top/2-25)
-      .text("Sample Correlation Scatterplot");
-      
-    text = "";
-    text += "N=" + js_data.num_overlap;
-    chart.append("text")
-      .attr("x", margin.left)
-      .attr("y", margin.top/2-5)
-      .text(text);
-    
-    text = "";
-    text += "r=" + js_data.r_value + "\t";
-    text += "p(r)=" + js_data.p_value;
-    chart.append("text")
-      .attr("x", margin.left)
-      .attr("y", margin.top/2+15)
-      .text(text);
-    
-    text = "";
-    text += "slope=" + js_data.slope + "\t";
-    text += "intercept=" + js_data.intercept;
-    chart.append("text")
-      .attr("x", margin.left)
-      .attr("y", margin.top/2+35)
-      .text(text);
-      
-    chart.append("text")
-      .attr("x", width/2)
-      .attr("y", height+margin.top+35)
-      .text(js_data.trait_1);
-      
-    chart.append("text")
-      .attr("x", 20)
-      .attr("y", height/2+margin.top+30)
-      .attr('transform', 'rotate(-90 20,' + (height/2+margin.top+30) + ')')
-      .text(js_data.trait_2);
+  })();
+
+  root.Scatter_Plot = Scatter_Plot;
+
+}).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/show_corr.coffee b/wqflask/wqflask/static/new/javascript/show_corr.coffee
new file mode 100644
index 00000000..727d3d86
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/show_corr.coffee
@@ -0,0 +1,4 @@
+root = exports ? this
+
+$ ->
+    root.scatter_plot = new Scatter_Plot()
diff --git a/wqflask/wqflask/static/new/javascript/show_corr.js b/wqflask/wqflask/static/new/javascript/show_corr.js
new file mode 100644
index 00000000..0a866548
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/show_corr.js
@@ -0,0 +1,11 @@
+// Generated by CoffeeScript 1.6.1
+(function() {
+  var root;
+
+  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+  $(function() {
+    return root.scatter_plot = new Scatter_Plot();
+  });
+
+}).call(this);