Committer: Lei Yan <lei@penguin.uthsc.edu>

On branch master

7 files changed, 156 insertions, 157 deletions

diff --git a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee
index 92a5c600..29a0e8f7 100644
--- a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee
+++ b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.coffee
@@ -1,61 +1,67 @@
-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
+root = exports ? this
 
-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")
+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
 
-# 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
+        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 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
+        # 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 4b34a09b..df1e62b6 100644
--- a/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js
+++ b/wqflask/wqflask/static/new/javascript/corr_scatter_plot.js
@@ -1,100 +1,77 @@
 // Generated by CoffeeScript 1.6.1
 (function() {
-  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);
+  var Scatter_Plot, root;
+
+  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+  Scatter_Plot = (function() {
+
+    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);
+    }
+
+    return Scatter_Plot;
+
+  })();
+
+  root.Scatter_Plot = Scatter_Plot;
 
 }).call(this);
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
index 16590e26..af53bd09 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.coffee
@@ -104,7 +104,7 @@ $ ->
             defaults =
                 species: "mouse"
                 group: "BXD"
-                type: "Hippocampus"
+                type: "Hippocampus mRNA"
                 dataset: "HC_M2_0606_P"
 
         for item in [['species', 'group']
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
index 5c5b433a..3a2f044f 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu.js
@@ -111,7 +111,7 @@
         defaults = {
           species: "mouse",
           group: "BXD",
-          type: "Hippocampus",
+          type: "Hippocampus mRNA",
           dataset: "HC_M2_0606_P"
         };
       }
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);
diff --git a/wqflask/wqflask/templates/corr_scatter_plot.html b/wqflask/wqflask/templates/corr_scatter_plot.html
index 490024ec..3ee1817c 100644
--- a/wqflask/wqflask/templates/corr_scatter_plot.html
+++ b/wqflask/wqflask/templates/corr_scatter_plot.html
@@ -41,11 +41,12 @@
 {% block js %}
     <script>
 		js_data = {{ js_data | safe }};
-	</script>
+    </script>
     <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
 	<script language="javascript" type="text/javascript" src="http://bgrins.github.io/spectrum/spectrum.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 	<script language="javascript" type="text/javascript" src="/static/new/javascript/corr_scatter_plot.js"></script>
+	<script language="javascript" type="text/javascript" src="/static/new/javascript/show_corr.js"></script>
     <script>
 		$("#circle_color").spectrum({
 			color: "{{circle_color}}",