- Added z-score transformation

- Added text indicating which transformation has been applied

5 files changed, 51 insertions, 16 deletions

diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 4e4c7705..932260de 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -12,6 +12,7 @@ from collections import OrderedDict
 import redis
 Redis = redis.StrictRedis()
 
+import numpy as np
 import scipy.stats as ss
 
 from flask import Flask, g
@@ -138,6 +139,7 @@ class ShowTrait(object):
         self.make_sample_lists()
 
         self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
+        self.z_scores = get_z_scores(self.sample_groups)
 
         # Todo: Add back in the ones we actually need from below, as we discover we need them
         hddn = OrderedDict()
@@ -226,6 +228,7 @@ class ShowTrait(object):
                        attribute_names = self.sample_groups[0].attributes,
                        num_values = self.num_values,
                        qnorm_values = self.qnorm_vals,
+                       zscore_values = self.z_scores,
                        sample_column_width = sample_column_width,
                        temp_uuid = self.temp_uuid)
         self.js_data = js_data
@@ -277,11 +280,15 @@ class ShowTrait(object):
             if self.dataset.group.species == "human":
                 primary_sample_names += other_sample_names
 
+            if other_sample_names:
+                primary_header = "%s Only" % (self.dataset.group.name)
+            else:
+                primary_header = "Samples"
             primary_samples = SampleList(dataset = self.dataset,
                                             sample_names=primary_sample_names,
                                             this_trait=self.this_trait,
                                             sample_group_type='primary',
-                                            header="%s Only" % (self.dataset.group.name))
+                                            header=primary_header)
 
             if other_sample_names and self.dataset.group.species != "human" and self.dataset.group.name != "CFW":
                 parent_f1_samples = None
@@ -292,13 +299,11 @@ class ShowTrait(object):
                 if parent_f1_samples:
                     other_sample_names = parent_f1_samples + other_sample_names
 
-                logger.debug("other_sample_names:", other_sample_names)
-
                 other_samples = SampleList(dataset=self.dataset,
                                             sample_names=other_sample_names,
                                             this_trait=self.this_trait,
                                             sample_group_type='other',
-                                            header="Non-%s" % (self.dataset.group.name))
+                                            header="Other")
 
                 self.sample_groups = (primary_samples, other_samples)
             else:
@@ -360,17 +365,19 @@ def get_z_scores(sample_groups):
             except:
                 continue
 
-        qnorm_vals = normf(trait_vals)
-        qnorm_vals_with_x = []
+        zscores = ss.mstats.zscore(np.array(trait_vals)).tolist()
+        zscores_with_x = []
         counter = 0
         for sample in sample_type.sample_list:
             if sample.display_value == "x":
-                qnorm_vals_with_x.append("x")
+                zscores_with_x.append("x")
             else:
-                qnorm_vals_with_x.append(qnorm_vals[counter])
+                zscores_with_x.append("%0.3f" % zscores[counter])
                 counter += 1
 
-        qnorm_by_group.append(qnorm_vals_with_x)
+        zscore_by_group.append(zscores_with_x)
+
+    return zscore_by_group
 
 def get_nearest_marker(this_trait, this_db):
     this_chr = this_trait.locus_chr
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index e985078b..9bbcd560 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -557,6 +557,7 @@ block_outliers = function() {
 $('#block_outliers').click(block_outliers);
 reset_samples_table = function() {
   $('input[name="transform"]').val("");
+  $('span[name="transform_text"]').text("")
   return $('.trait_value_input').each((function(_this) {
     return function(_index, element) {
       $(element).val($(element).data('value'));
@@ -623,26 +624,52 @@ qnorm_data = function() {
   })(this));
 };
 
+zscore_data = function() {
+  return $('.edit_sample_value').each((function(_this) {
+    return function(_index, element) {
+      current_value = parseFloat($(element).data("value")) + 1;
+      if(isNaN(current_value)) {
+        return current_value
+      } else {
+        $(element).val($(element).data("zscore"));
+        return $(element).data("zscore");
+      }
+    };
+  })(this));
+};
+
 normalize_data = function() {
   if ($('#norm_method option:selected').val() == 'log2'){
     if ($('input[name="transform"]').val() != "log2") {
       log_normalize_data()
       $('input[name="transform"]').val("log2")
+      $('span[name="transform_text"]').text(" - log2 transformed")
     }
   }
   else if ($('#norm_method option:selected').val() == 'sqrt'){
     if ($('input[name="transform"]').val() != "sqrt") {
       sqrt_normalize_data()
       $('input[name="transform"]').val("sqrt")
+      $('span[name="transform_text"]').text(" - Square Root transformed")
     }
   }
   else if ($('#norm_method option:selected').val() == 'invert'){
     invert_data()
+    $('input[name="transform"]').val("inverted")
+    $('span[name="transform_text"]').text(" - Inverted")
   }
   else if ($('#norm_method option:selected').val() == 'qnorm'){
     if ($('input[name="transform"]').val() != "qnorm") {
       qnorm_data()
       $('input[name="transform"]').val("qnorm")
+      $('span[name="transform_text"]').text(" - Quantile Normalized")
+    }
+  }
+  else if ($('#norm_method option:selected').val() == 'zscore'){
+    if ($('input[name="transform"]').val() != "zscore") {
+      zscore_data()
+      $('input[name="transform"]').val("zscore")
+      $('span[name="transform_text"]').text(" - Z-Scores")
     }
   }
 }
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 3bd57f89..e4feb817 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -294,9 +294,9 @@
                       'data': null,
                       'render': function(data, type, row, meta) {
                         if (data.value == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
+                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=6 maxlength=6>'
                         } else {
-                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
+                          return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id)] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id)] + '" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=6 maxlength=6>'
                         }
                       }
                     }{% if sample_groups[0].se_exists() %},
@@ -315,9 +315,9 @@
                       'data': null,
                       'render': function(data, type, row, meta) {
                         if (data.variance == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
+                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="x" size=6 maxlength=6>'
                         } else {
-                          return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
+                          return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6 maxlength=6>'
                         }
                       }
                     }{% endif %}{% if has_num_cases %},
@@ -328,9 +328,9 @@
                       'data': null,
                       'render': function(data, type, row, meta) {
                         if (data.num_cases == null) {
-                          return '<input type="text" data-value="x" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
+                          return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>'
                         } else {
-                          return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
+                          return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>'
                         }
                       }
                     }{% endif %}{% if sample_groups[0].attributes|length > 0 %}{% for attribute in sample_groups[0].attributes|sort() %},
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index a5e42fdb..667d557c 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -13,7 +13,7 @@
     {% for sample_type in sample_groups %}
         {% set outer_loop = loop %}
         <div class="sample_group" style="width:{{ trait_table_width }};">
-            <h3>{{ sample_type.header }}</h3>
+            <h3>{{ sample_type.header }}<span name="transform_text"></span></h3>
             <hr style="margin-top: 4px; margin-bottom: 10px; height: 1px; background-color: #A9A9A9;">
             <div id="table_container">
             <table class="table-hover table-striped cell-border" id="samples_{{ sample_type.sample_group_type }}" style="float: left; width:100%;">
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 04ceaeaf..6803da58 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -52,6 +52,7 @@
               <input type="button" id="normalize" class="btn btn-default" value="Normalize">
               <select id="norm_method" class="select optional span2">
                 <option value="log2">Log2</option>
+                <option value="zscore">Z-score</option>
                 <option value="qnorm">Quantile</option>
                 <option value="sqrt">Square Root</option>
                 <option value="invert">Invert +/-</option>