Switched to plotly probability plot

Removed a variety of scripts that weren't being used on the trait page

3 files changed, 248 insertions, 17 deletions

diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
new file mode 100644
index 00000000..49fd53b1
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -0,0 +1,246 @@
+// 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 = 600;
+    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);
+    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;
+    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]
+    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]
+    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'), make_data('samples_all')];
+    console.log("THE DATA IS:", data);
+    x_values = {}
+    y_values = {}
+    point_names = {}
+    for (i = 0; i < 3; i++){
+      these_x_values = []
+      these_y_values = []
+      these_names = []
+      for (j = 0; j < data[i].values.length; j++){
+        these_x_values.push(data[i].values[j].x)
+        these_y_values.push(data[i].values[j].y)
+        these_names.push(data[i].values[j].name)
+      }
+      if (i == 0){
+        x_values['samples_primary'] = these_x_values
+        y_values['samples_primary'] = these_y_values
+        point_names['samples_primary'] = these_names
+      } else if (i == 1) {
+        x_values['samples_other'] = these_x_values
+        y_values['samples_other'] = these_y_values
+        point_names['samples_other'] = these_names
+      } else {
+        x_values['samples_all'] = these_x_values
+        y_values['samples_all'] = these_y_values
+        point_names['samples_all'] = these_names
+      }
+    }
+
+    intercept_line = {}
+
+    if (sample_group == "samples_primary"){
+        first_x = Math.floor(x_values['samples_primary'][0])
+        first_x = first_x - first_x*0.1
+        last_x = Math.ceil(x_values['samples_primary'][x_values['samples_primary'].length - 1])
+        last_x = last_x + last_x*0.1
+        first_value = data[0].intercept + data[0].slope * first_x
+        last_value = data[0].intercept + data[0].slope * last_x
+        intercept_line['samples_primary'] = [[first_x, last_x], [first_value, last_value]]
+    } else if (sample_group == "samples_other") {
+        first_x = Math.floor(x_values['samples_other'][0])
+        first_x = first_x - first_x*0.1
+        last_x = Math.ceil(x_values['samples_other'][x_values['samples_other'].length - 1])
+        last_x = last_x + last_x*0.1
+        first_value = data[1].intercept + data[1].slope * first_x
+        last_value = data[1].intercept + data[1].slope * last_x
+        intercept_line['samples_other'] = [[first_x, last_x], [first_value, last_value]]
+    } else {
+        first_x = Math.floor(x_values['samples_all'][0])
+        first_x = first_x - first_x*0.1
+        last_x = Math.ceil(x_values['samples_all'][x_values['samples_all'].length - 1])
+        first_value = data[2].intercept + data[2].slope * first_x
+        last_x = last_x + last_x*0.1
+        last_value = data[2].intercept + data[2].slope * last_x
+        intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]]
+    }
+
+    var layout = {
+        margin: {
+            l: 50,
+            r: 30,
+            t: 30,
+            b: 80
+        },
+        xaxis: {
+            range: [first_x, last_x],
+            zeroline: false,
+            visible: true,
+            linecolor: 'black',
+            linewidth: 1,
+        },
+        yaxis: {
+            zeroline: false,
+            visible: true,
+            linecolor: 'black',
+            linewidth: 1,
+        }
+    }
+
+    var primary_trace = {
+        x: x_values['samples_primary'],
+        y: y_values['samples_primary'],
+        mode: 'markers',
+        type: 'scatter',
+        name: js_data.sample_group_types['samples_primary'],
+        text: point_names['samples_primary']
+    }
+    if ("samples_other" in js_data.sample_group_types) {
+        var other_trace = {
+            x: x_values['samples_other'],
+            y: y_values['samples_other'],
+            mode: 'markers',
+            type: 'scatter',
+            name: js_data.sample_group_types['samples_other'],
+            text: point_names['samples_other']
+        }
+    }
+
+    if (sample_group == "samples_primary"){
+        var primary_intercept_trace = {
+            x: intercept_line['samples_primary'][0],
+            y: intercept_line['samples_primary'][1],
+            mode: 'lines',
+            type: 'scatter',
+            name: 'Intercept',
+        }
+    } else if (sample_group == "samples_other"){
+        var other_intercept_trace = {
+            x: intercept_line['samples_other'][0],
+            y: intercept_line['samples_other'][1],
+            mode: 'lines',
+            type: 'scatter',
+            name: 'Intercept',
+        }
+    } else {
+        var all_intercept_trace = {
+            x: intercept_line['samples_all'][0],
+            y: intercept_line['samples_all'][1],
+            mode: 'lines',
+            type: 'scatter',
+            name: 'Intercept',
+        }
+    }
+
+    if (sample_group == "samples_primary"){
+        var data = [primary_trace, primary_intercept_trace]
+    } else if (sample_group == "samples_other"){
+        var data = [other_trace, other_intercept_trace]
+    } else {
+        var data = [primary_trace, other_trace, all_intercept_trace]
+    }
+
+    console.log("TRACE:", data)
+    Plotly.newPlot('prob_plot_div', data, layout)
+  };
+
+  root.redraw_prob_plot_impl = redraw_prob_plot;
+
+}).call(this);
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index dd4325e7..5d128b4a 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -133,34 +133,21 @@
     <script type="text/javascript" src="/static/new/js_external/jstat.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/shapiro-wilk.js"></script>
     <script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
-    <script type="text/javascript" src="/static/new/js_external/saveSvgAsPng.js"></script>
     <script type="text/javascript" src="/static/new/javascript/colorbrewer.js"></script>
 
     <script type="text/javascript" src="/static/new/javascript/stats.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/box.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/bar_chart.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/histogram.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/box_plot.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/scatterplot.js"></script>
     <script type="text/javascript" src="/static/new/javascript/scatter-matrix.js"></script>
-    <script type="text/javascript" src="/static/new/javascript/draw_probability_plot.js"></script>
-    <!--<script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>-->
+    <script type="text/javascript" src="/static/new/javascript/plotly_probability_plot.js"></script>
     <script type="text/javascript" src="/static/new/javascript/compare_traits_scatterplot.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/get_covariates_from_collection.js"></script>
 
     <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
     <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
     <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/FileSaver.js/FileSaver.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/libs/Blob.js/BlobBuilder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.standard_fonts_metrics.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/jsPDF/jspdf.plugin.from_html.js"></script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
     <script type="text/javascript" charset="utf-8">
             
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index aa95b083..09df3245 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -110,9 +110,7 @@
                         {% endif %}
 
                         <div id="prob_plot_container">
-                            <div id="prob_plot_title"></div>
-                            <svg></svg>
-                            <!--<div id="prob_plot_div"></div>-->
+                            <div id="prob_plot_div"></div>
                         </div>
                         <div id="shapiro_wilk_text"></div>
                         <div>