From b964a8b732c1066978ce88073c009803f36a9173 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 6 Jul 2018 16:27:46 +0000
Subject: Added square root transform options

Figures now correctly rescale when transforms are applied

Fixed height of probability plot

Removed some text related to pylmm since it's currently not being used
---
 .../static/new/javascript/draw_probability_plot.js |  2 +-
 .../new/javascript/plotly_probability_plot.js      |  2 +-
 .../wqflask/static/new/javascript/show_trait.js    | 25 +++++++++++++++++++++-
 .../wqflask/templates/show_trait_edit_data.html    |  1 +
 .../templates/show_trait_mapping_tools.html        |  4 ++++
 5 files changed, 31 insertions(+), 3 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index f23dad0c..3d756303 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -26,7 +26,7 @@
   redraw_prob_plot = function(samples, sample_group) {
     var container, h, margin, totalh, totalw, w;
     h = 600;
-    w = 600;
+    w = 500;
     margin = {
       left: 60,
       top: 40,
diff --git a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
index 49fd53b1..185de8a9 100644
--- a/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/plotly_probability_plot.js
@@ -25,7 +25,7 @@
 
   redraw_prob_plot = function(samples, sample_group) {
     var container, h, margin, totalh, totalw, w;
-    h = 600;
+    h = 370;
     w = 600;
     margin = {
       left: 60,
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5e2ecc33..d641dc67 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -247,6 +247,9 @@
       }
       root.bar_data[0]['x'] = trait_samples
       Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout);
+      Plotly.relayout('bar_chart', {
+          'yaxis.autorange': true
+      });
     };
 
     redraw_box_plot = function() {
@@ -564,7 +567,7 @@
     log_normalize_data = function() {
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
-          current_value = $(element).data("value");
+          current_value = parseFloat($(element).data("value")) + 1;
           if(isNaN(current_value)) {
             return current_value
           } else {
@@ -575,6 +578,20 @@
       })(this));
     };
 
+    sqrt_normalize_data = function() {
+      return $('.trait_value_input').each((function(_this) {
+        return function(_index, element) {
+          current_value = parseFloat($(element).data("value")) + 1;
+          if(isNaN(current_value)) {
+            return current_value
+          } else {
+            $(element).val(Math.sqrt(current_value).toFixed(3));
+            return Math.sqrt(current_value).toFixed(3)
+          }
+        };
+      })(this));
+    };
+
     qnorm_data = function() {
       return $('.trait_value_input').each((function(_this) {
         return function(_index, element) {
@@ -596,6 +613,12 @@
           $('input[name="transform"]').val("log2")
         }
       }
+      else if ($('#norm_method option:selected').val() == 'sqrt'){
+        if ($('input[name="transform"]').val() != "sqrt") {
+          sqrt_normalize_data()
+          $('input[name="transform"]').val("sqrt")
+        }
+      }
       else if ($('#norm_method option:selected').val() == 'qnorm'){
         if ($('input[name="transform"]').val() != "qnorm") {
           qnorm_data()
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 482d1d88..ac2f1078 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -56,6 +56,7 @@
               <select id="norm_method" class="select optional span2">
                 <option value="log2">Log2</option>
                 <option value="qnorm">Quantile</option>
+                <option value="sqrt">Square Root</option>
               </select>
               </div>
               <!--
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index a54b595b..53b6646c 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -14,9 +14,11 @@
                 <li>
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
+<!--
                 <li>
                     <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
+-->
                 {% endif %}
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
@@ -330,8 +332,10 @@
              <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
              <dt>R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+<!--
              <dt>pyLMM</dt>
              <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
+-->
              {% endif %}
         </dl>
     </div>
-- 
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