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-rw-r--r--wqflask/wqflask/static/new/javascript/draw_probability_plot.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/plotly_probability_plot.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js25
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html4
5 files changed, 31 insertions, 3 deletions
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>