merge changes

1 files changed, 136 insertions, 0 deletions

diff --git a/gn2/wqflask/static/new/javascript/draw_probability_plot.js b/gn2/wqflask/static/new/javascript/draw_probability_plot.js
new file mode 100644
index 00000000..1b944d4f
--- /dev/null
+++ b/gn2/wqflask/static/new/javascript/draw_probability_plot.js
@@ -0,0 +1,136 @@
+// Generated by CoffeeScript 1.9.2
+(function() {
+  var get_z_scores, redraw_prob_plot, root;
+
+  root = typeof exports !== "undefined" && exports !== null ? exports : this;
+
+  get_z_scores = function(n) {
+    var i, j, osm_uniform, ref, x;
+    osm_uniform = new Array(n);
+    osm_uniform[n - 1] = Math.pow(0.5, 1.0 / n);
+    osm_uniform[0] = 1 - osm_uniform[n - 1];
+    for (i = j = 1, ref = n - 2; 1 <= ref ? j <= ref : j >= ref; i = 1 <= ref ? ++j : --j) {
+      osm_uniform[i] = (i + 1 - 0.3175) / (n + 0.365);
+    }
+    return (function() {
+      var k, len, results;
+      results = [];
+      for (k = 0, len = osm_uniform.length; k < len; k++) {
+        x = osm_uniform[k];
+        results.push(jStat.normal.inv(x, 0, 1));
+      }
+      return results;
+    })();
+  };
+
+  redraw_prob_plot = function(samples, sample_group) {
+    var container, h, margin, totalh, totalw, w;
+    h = 600;
+    w = 500;
+    margin = {
+      left: 60,
+      top: 40,
+      right: 40,
+      bottom: 40,
+      inner: 5
+    };
+    totalh = h + margin.top + margin.bottom;
+    totalw = w + margin.left + margin.right;
+    container = $("#prob_plot_container");
+    container.width(totalw);
+    container.height(totalh);
+    return nv.addGraph((function(_this) {
+      return function() {
+        var W, all_samples, chart, data, intercept, make_data, names, pvalue, pvalue_str, slope, sorted_names, sorted_values, sw_result, test_str, x, z_scores;
+        chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range());
+        chart.pointRange([50, 50]);
+        chart.legend.updateState(false);
+        chart.xAxis.axisLabel("Expected Z score").axisLabelDistance(20).tickFormat(d3.format('.02f'));
+        chart.tooltipContent(function(obj) {
+          return '<b style="font-size: 20px">' + obj.point.name + '</b>';
+        });
+        all_samples = samples[sample_group];
+        names = (function() {
+          var j, len, ref, results;
+          ref = _.keys(all_samples);
+          results = [];
+          for (j = 0, len = ref.length; j < len; j++) {
+            x = ref[j];
+            if (all_samples[x] !== null) {
+              results.push(x);
+            }
+          }
+          return results;
+        })();
+        sorted_names = names.sort(function(x, y) {
+          return all_samples[x].value - all_samples[y].value;
+        });
+        max_decimals = 0
+        sorted_values = (function() {
+          var j, len, results;
+          results = [];
+          for (j = 0, len = sorted_names.length; j < len; j++) {
+            x = sorted_names[j];
+            results.push(all_samples[x].value);
+            if (all_samples[x].value.countDecimals() > max_decimals) {
+                max_decimals = all_samples[x].value.countDecimals()-1
+            }
+          }
+          return results;
+        })();
+        //ZS: 0.1 indicates buffer, increase to increase buffer
+        y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1]
+        chart.yDomain(y_domain)
+        chart.yAxis.axisLabel("Trait value").axisLabelDistance(10).tickFormat(d3.format('.0'+max_decimals.toString()+'f'));
+        sw_result = ShapiroWilkW(sorted_values);
+        W = sw_result.w.toFixed(3);
+        pvalue = sw_result.p.toFixed(3);
+        pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>";
+        test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")";
+        z_scores = get_z_scores(sorted_values.length);
+        //ZS: 0.1 indicates buffer, increase to increase buffer
+        x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1]
+        chart.xDomain(x_domain)
+        slope = jStat.stdev(sorted_values);
+        intercept = jStat.mean(sorted_values);
+        make_data = function(group_name) {
+          var sample, value, z_score;
+          return {
+            key: js_data.sample_group_types[group_name],
+            slope: slope,
+            intercept: intercept,
+            values: (function() {
+              var j, len, ref, ref1, results;
+              ref = _.zip(get_z_scores(sorted_values.length), sorted_values, sorted_names);
+              results = [];
+              for (j = 0, len = ref.length; j < len; j++) {
+                ref1 = ref[j], z_score = ref1[0], value = ref1[1], sample = ref1[2];
+                if (sample in samples[group_name]) {
+                  results.push({
+                    x: z_score,
+                    y: value,
+                    name: sample
+                  });
+                }
+              }
+              return results;
+            })()
+          };
+        };
+        data = [make_data('samples_primary'), make_data('samples_other')];
+        d3.select("#prob_plot_container svg").datum(data).call(chart);
+        if (js_data.trait_symbol != null) {
+            $("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>");
+        } else {
+            $("#prob_plot_title").html("<h3>" + js_data.trait_id + "</h3>");
+        }
+        $("#shapiro_wilk_text").html(test_str)
+        $("#prob_plot_container .nv-legendWrap").toggle(sample_group === "samples_all");
+        return chart;
+      };
+    })(this));
+  };
+
+  root.redraw_prob_plot_impl = redraw_prob_plot;
+
+}).call(this);