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-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py4
-rw-r--r--wqflask/maintenance/geno_to_json.py6
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py5
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py8
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css4
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json96
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js80
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js29
-rw-r--r--wqflask/wqflask/static/new/javascript/stats.js12
-rw-r--r--wqflask/wqflask/templates/mapping_results.html5
-rw-r--r--wqflask/wqflask/templates/search_result_page.html9
-rw-r--r--wqflask/wqflask/templates/show_trait.html33
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html9
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html12
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html67
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html10
-rw-r--r--wqflask/wqflask/templates/show_trait_transform_and_filter.html79
17 files changed, 322 insertions, 146 deletions
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index ad0eb036..b53f5dda 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -54,8 +54,8 @@ class GenerateKinshipMatrices(object):
if __name__=="__main__":
- Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
- Bimbam_Directory = """/home/zas1024/genotype_files/genotype/bimbam/"""
+ Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
+ Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
#./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD \ No newline at end of file
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 789a1691..9579812a 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -24,6 +24,8 @@ import simplejson as json
from pprint import pformat as pf
+#from utility.tools import flat_files
+
class EmptyConfigurations(Exception): pass
@@ -183,8 +185,8 @@ class ConvertGenoFile(object):
if __name__=="__main__":
- Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
- New_Geno_Directory = """/home/zas1024/genotype_files/genotype/json/"""
+ Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
+ New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
#Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
#Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
#convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 31d47ff2..6d9f07a0 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -63,10 +63,7 @@ class SampleList(object):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
- if sample_group_type == 'primary':
- sample.this_id = "Primary_" + str(counter)
- else:
- sample.this_id = "Other_" + str(counter)
+ sample.this_id = str(counter)
#### For extra attribute columns; currently only used by several datasets - Zach
if self.sample_attribute_values:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 34447853..7d6dd74e 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -153,7 +153,8 @@ class ShowTrait(object):
hddn['group'] = self.temp_group
hddn['species'] = self.temp_species
hddn['use_outliers'] = False
- hddn['method'] = "pylmm"
+ hddn['method'] = "gemma"
+ hddn['selected_chr'] = -1
hddn['mapping_display_all'] = True
hddn['suggestive'] = 0
hddn['num_perm'] = 0
@@ -182,6 +183,11 @@ class ShowTrait(object):
self.sample_group_types['samples_primary'] = self.dataset.group.name
sample_lists = [group.sample_list for group in self.sample_groups]
+ #ZS: Get list of chromosomes to select for mapping
+ self.chr_list = [["All", -1]]
+ for i, this_chr in enumerate(self.species.chromosomes.chromosomes):
+ self.chr_list.append([self.species.chromosomes.chromosomes[this_chr].name, i])
+
self.genofiles = get_genofiles(self.dataset)
self.has_num_cases = has_num_cases(self.this_trait)
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index aa47d13f..c03b6103 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -27,6 +27,10 @@ table.dataTable thead .sorting_desc {
background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
}
+table.dataTable thead th {
+ padding: 4px 18px 4px 10px;
+}
+
table.dataTable tbody td {
padding: 3px 20px 1px 10px;
}
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 9c806a7f..72008225 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1557,6 +1557,42 @@
]
]
},
+ "AIL-LGSM-F34-A": {
+ "Phenotypes": [
+ [
+ "None",
+ "AIL-LGSM-F34-APublish",
+ "AIL-LGSM-F34-A Phenotypes"
+ ]
+ ]
+ },
+ "AIL-LGSM-F34-F39-43-GBS": {
+ "Phenotypes": [
+ [
+ "None",
+ "AIL-LGSM-F34-F39-43-GBSPublish",
+ "AIL-LGSM-F34-F39-43-GBS Phenotypes"
+ ]
+ ]
+ },
+ "AIL-LGSM-F34-GBS": {
+ "Phenotypes": [
+ [
+ "None",
+ "AIL-LGSM-F34-GBSPublish",
+ "AIL-LGSM-F34-GBS Phenotypes"
+ ]
+ ]
+ },
+ "AIL-LGSM-F39-43-GBS": {
+ "Phenotypes": [
+ [
+ "None",
+ "AIL-LGSM-F39-43-GBSPublish",
+ "AIL-LGSM-F39-43-GBS Phenotypes"
+ ]
+ ]
+ },
"AKXD": {
"Genotypes": [
[
@@ -2591,6 +2627,11 @@
],
"Liver mRNA": [
[
+ "857",
+ "EPFLMouseLiverCDHFDRMA0818",
+ "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+ ],
+ [
"859",
"EPFLMouseLiverCDRMA0818",
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
@@ -2621,11 +2662,6 @@
"NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
],
[
- "857",
- "EPFLMouseLiverCDHFDRMA0818",
- "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
- ],
- [
"430",
"EPFLMouseLiverRMA0413",
"EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
@@ -2641,6 +2677,11 @@
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
],
[
+ "848",
+ "EPFLMouseLiverHFCEx0413",
+ "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+ ],
+ [
"433",
"EPFLMouseLiverBothExRMA0413",
"EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2651,11 +2692,6 @@
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
],
[
- "848",
- "EPFLMouseLiverHFCEx0413",
- "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
- ],
- [
"700",
"UTHSC-VGX_MmBXDHepatocytesRMA1014",
"UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -4002,6 +4038,22 @@
"AIL Advanced Intercross Line"
],
[
+ "AIL-LGSM-F34-A",
+ "AIL LGSM F34 (Array)"
+ ],
+ [
+ "AIL-LGSM-F34-GBS",
+ "AIL LGSM F34 (GBS)"
+ ],
+ [
+ "AIL-LGSM-F34-F39-43-GBS",
+ "AIL LGSM F34 and F39-43 (GBS)"
+ ],
+ [
+ "AIL-LGSM-F39-43-GBS",
+ "AIL LGSM F39-43 (GBS)"
+ ],
+ [
"AKXD",
"AKXD RI Family"
],
@@ -4929,6 +4981,30 @@
"Striatum mRNA"
]
],
+ "AIL-LGSM-F34-A": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
+ "AIL-LGSM-F34-F39-43-GBS": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
+ "AIL-LGSM-F34-GBS": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
+ "AIL-LGSM-F39-43-GBS": [
+ [
+ "Phenotypes",
+ "Phenotypes"
+ ]
+ ],
"AKXD": [
[
"Genotypes",
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index df86e764..717d98b9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -417,16 +417,27 @@
}
console.log("towards end:", sample_sets);
update_stat_values(sample_sets);
- console.log("redrawing histogram");
- redraw_histogram();
- console.log("redrawing bar chart");
- redraw_bar_chart();
- console.log("redrawing box plot");
- redraw_box_plot();
- console.log("redrawing violin plot");
- redraw_violin_plot();
- console.log("redrawing probability plot");
- return redraw_prob_plot();
+
+ if ($('#histogram').hasClass('js-plotly-plot')){
+ console.log("redrawing histogram");
+ redraw_histogram();
+ }
+ if ($('#bar_chart').hasClass('js-plotly-plot')){
+ console.log("redrawing bar chart");
+ redraw_bar_chart();
+ }
+ if ($('#box_plot').hasClass('js-plotly-plot')){
+ console.log("redrawing box plot");
+ redraw_box_plot();
+ }
+ if ($('#violin_plot').hasClass('js-plotly-plot')){
+ console.log("redrawing violin plot");
+ redraw_violin_plot();
+ }
+ if ($('#prob_plot_div').hasClass('js-plotly-plot')){
+ console.log("redrawing probability plot");
+ return redraw_prob_plot();
+ }
};
show_hide_outliers = function() {
var label;
@@ -853,7 +864,13 @@
}
};
root.bar_layout = layout
- Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options)
+ $('.bar_chart_tab').click(function() {
+ if ($('#bar_chart').hasClass('js-plotly-plot')){
+ redraw_bar_chart();
+ } else {
+ Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options)
+ }
+ });
}
if (full_sample_lists.length > 1) {
@@ -957,11 +974,18 @@
]
}
- obj = {
+ box_obj = {
data: box_data,
layout: root.box_layout
}
- Plotly.newPlot('box_plot', obj, root.modebar_options);
+
+ $('.box_plot_tab').click(function() {
+ if ($('#box_plot').hasClass('js-plotly-plot')){
+ redraw_box_plot();
+ } else {
+ Plotly.newPlot('box_plot', box_obj, root.modebar_options);
+ }
+ });
// Violin Plot
@@ -1066,12 +1090,18 @@
]
}
- obj = {
+ violin_obj = {
data: violin_data,
layout: root.violin_layout
}
- Plotly.plot('violin_plot', obj, root.modebar_options)
+ $('.violin_plot_tab').click(function() {
+ if ($('#violin_plot').hasClass('js-plotly-plot')){
+ redraw_violin_plot();
+ } else {
+ Plotly.plot('violin_plot', violin_obj, root.modebar_options);
+ }
+ });
// Histogram
var hist_trace = {
@@ -1091,9 +1121,16 @@
b: 60
}
};
- Plotly.newPlot('histogram', data, layout, root.modebar_options)
- update_histogram_width()
+ $('.histogram_tab').click(function() {
+ if ($('#histogram').hasClass('js-plotly-plot')){
+ redraw_histogram();
+ update_histogram_width();
+ } else {
+ Plotly.newPlot('histogram', data, layout, root.modebar_options)
+ update_histogram_width()
+ }
+ });
$('.histogram_samples_group').val(root.stats_group);
$('.histogram_samples_group').change(function() {
@@ -1119,13 +1156,18 @@
root.prob_plot_group = 'samples_primary';
$('.prob_plot_samples_group').val(root.prob_plot_group);
+ $('.prob_plot_tab').click(function() {
+ return redraw_prob_plot();
+ });
$('.prob_plot_samples_group').change(function() {
root.prob_plot_group = $(this).val();
return redraw_prob_plot();
});
- make_table();
- edit_data_change();
+ $('.stats_panel').click(function() {
+ make_table();
+ edit_data_change();
+ });
$('#edit_sample_lists').change(edit_data_change);
$('.edit_sample_value').change(edit_data_change);
$('#block_by_index').click(edit_data_change);
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index daa5b3f2..4e82fff2 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -154,36 +154,12 @@
};
})(this));
- $("#pylmm_mapping_compute").on("mouseover", (function(_this) {
- return function() {
- if ($(".outlier").length && $(".outlier-alert").length < 1) {
- return showalert(outlier_text, "alert-success outlier-alert");
- }
- };
- })(this));
-
- $("#pylmm_compute").on("click", (function(_this) {
- return function() {
- var form_data, url;
- //$("#progress_bar_container").modal();
- url = "/loading";
- $('input[name=method]').val("pylmm");
- $('input[name=genofile]').val($('#genofile_pylmm').val());
- $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
- $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
- form_data = $('#trait_data_form').serialize();
- console.log("form_data is:", form_data);
- return submit_special(url);
- //return do_ajax_post(url, form_data);
- };
- })(this));
-
$("#rqtl_geno_compute").on("click", (function(_this) {
return function() {
var form_data, url;
- //$("#progress_bar_container").modal();
url = "/loading";
$('input[name=method]').val("rqtl_geno");
+ $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
$('input[name=genofile]').val($('#genofile_rqtl_geno').val());
$('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
$('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
@@ -203,7 +179,6 @@
}
else {
return submit_special(url);
- //return do_ajax_post(url, form_data);
}
};
})(this));
@@ -214,6 +189,7 @@
console.log("RUNNING GEMMA");
url = "/loading";
$('input[name=method]').val("gemma");
+ $('input[name=selected_chr]').val($('#chr_gemma').val());
$('input[name=num_perm]').val(0);
$('input[name=genofile]').val($('#genofile_gemma').val());
$('input[name=maf]').val($('input[name=maf_gemma]').val());
@@ -230,6 +206,7 @@
//$("#progress_bar_container").modal();
url = "/loading";
$('input[name=method]').val("reaper");
+ $('input[name=selected_chr]').val($('#chr_reaper').val());
$('input[name=genofile]').val($('#genofile_reaper').val());
$('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
$('input[name=control_marker]').val($('input[name=control_reaper]').val());
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 4f99982e..356d1cb0 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -154,16 +154,4 @@ Stats = (function() {
})();
-bxd_only = new Stats([3, 5, 7, 8]);
-
-console.log("[xred] bxd_only mean:", bxd_only.mean());
-
-console.log("[xgreen] bxd_only median:", bxd_only.median());
-
-console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev());
-
-console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error());
-
-console.log("[xyellow] bxd_only min:", bxd_only.min());
-
window.Stats = Stats;
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 5fb2c95e..00d725ea 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -257,7 +257,7 @@
<div style="width: 100%;">
<h2>Interval Analyst</h2>
<div id="table_container">
- <table id="interval_analyst" class="table table-hover table-striped nowrap">
+ <table id="interval_analyst" class="table-hover table-striped cell-border" style="float: left; width:100%;">
<thead>
<tr>
{% for header in gene_table_header %}
@@ -355,9 +355,7 @@
"autoWidth": false,
"deferRender": true,
"bSortClasses": false,
- "scrollY": "600px",
"scrollCollapse": false,
- "scroller": true,
"paging": false
} );
@@ -372,7 +370,6 @@
"autoWidth": false,
"deferRender": true,
"bSortClasses": false,
- "scrollY": "600px",
"scrollCollapse": false,
"paging": false
} );
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 9ad8a53e..a325ec9f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -4,6 +4,7 @@
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css">
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
<!-- Start of body -->
@@ -84,9 +85,9 @@
<th></th>
{% for header in header_fields %}
{% if header == 'Max LRS' %}
- <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+ <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>
{% elif header == 'Additive Effect' %}
- <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+ <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>
{% else %}
<th data-export="{{header}}">{{header}}</th>
{% endif %}
@@ -99,9 +100,9 @@
<th></th>
{% for header in header_fields %}
{% if header == 'Max LRS' %}
- <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+ <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>
{% elif header == 'Additive Effect' %}
- <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+ <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>
{% else %}
<th data-export="{{header}}">{{header}}</th>
{% endif %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 8726226c..f5e81060 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -52,7 +52,7 @@
</div>
</div>
<div class="panel panel-default">
- <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
+ <div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
<h3 class="panel-title">
<span class="glyphicon glyphicon-chevron-down"></span> Statistics
</h3>
@@ -62,26 +62,38 @@
{% include 'show_trait_statistics.html' %}
</div>
</div>
- </div>
+ </div>
<div class="panel panel-default">
<div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree">
<h3 class="panel-title">
- <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations
+ <span class="glyphicon glyphicon-chevron-down"></span> Transform and Filter Data
</h3>
</div>
<div id="collapseThree" class="panel-collapse collapse in">
<div class="panel-body">
+ {% include 'show_trait_transform_and_filter.html' %}
+ </div>
+ </div>
+ </div>
+ <div class="panel panel-default">
+ <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour">
+ <h3 class="panel-title">
+ <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations
+ </h3>
+ </div>
+ <div id="collapseFour" class="panel-collapse collapse in">
+ <div class="panel-body">
{% include 'show_trait_calculate_correlations.html' %}
</div>
</div>
</div>
<div class="panel panel-default">
- <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour">
+ <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive">
<h3 class="panel-title">
<span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools
</h3>
</div>
- <div id="collapseFour" class="panel-collapse collapse in">
+ <div id="collapseFive" class="panel-collapse collapse in">
<div class="panel-body">
{% include 'show_trait_mapping_tools.html' %}
</div>
@@ -89,12 +101,12 @@
</div>
</div>
<div class="panel panel-default">
- <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive" aria-expanded="true">
+ <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseSix" aria-expanded="true">
<h3 class="panel-title">
<span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data
</h3>
</div>
- <div id="collapseFive" class="panel-collapse collapse" aria-expanded="true">
+ <div id="collapseSix" class="panel-collapse collapse" aria-expanded="true">
<div class="panel-body">
{% include 'show_trait_edit_data.html' %}
</div>
@@ -210,7 +222,7 @@
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
- "bDeferRender": true,
+ "deferRender": false,
"bSortClasses": false,
"scrollY": "600px",
"scrollCollapse": false,
@@ -221,7 +233,7 @@
} );
{% else %}
-
+
$('#samples_primary, #samples_other').DataTable( {
"columns": [
{ "bSortable": false, "width": "8%" },
@@ -242,7 +254,7 @@
"iDisplayLength": -1,
"autoWidth": true,
"bLengthChange": true,
- "bDeferRender": true,
+ "deferRender": false,
"bSortClasses": false,
"scrollY": "600px",
"scrollCollapse": false,
@@ -251,6 +263,7 @@
},
"paging": false
} );
+
{% endif %}
var slider = document.getElementById('p_range_slider');
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c1f8f824..0192bff1 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -5,10 +5,6 @@
</tr>
{% if this_trait.dataset.type == 'Publish' %}
<tr>
- <td>Tissue</td>
- <td>{{ this_trait.dataset.tissue }}</td>
- </tr>
- <tr>
<td>Phenotype</td>
<td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td>
</tr>
@@ -24,6 +20,11 @@
<td>Journal</td>
<td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td>
</tr>
+ {% else %}
+ <tr>
+ <td>Tissue</td>
+ <td>{{ this_trait.dataset.tissue }}</td>
+ </tr>
{% endif %}
{% if this_trait.dataset.type == 'ProbeSet' %}
{% if this_trait.symbol != None %}
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index cfcf2ce5..ab134663 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,6 +1,7 @@
<div>
<!--<h2>Review and Edit Data</h2>-->
+<!--
<div class="well form-horizontal">
<fieldset id="showHideOptions">
<legend>Block samples</legend>
@@ -59,11 +60,6 @@
<option value="sqrt">Square Root</option>
</select>
</div>
- <!--
- {% if sample_groups[0].sample_qnorm is not none %}
- <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
- {% endif %}
- -->
</div>
</fieldset>
<br>
@@ -81,7 +77,7 @@
</div>
</div>
<br>
-
+-->
<!--<div id="edit_sample_lists">-->
{% for sample_type in sample_groups %}
@@ -94,7 +90,7 @@
<thead>
<tr>
<th></th>
- <th>Index</th>
+ <th>ID</th>
<th>Sample</th>
<th style="text-align: right;">Value</th>
{% if sample_type.se_exists() %}
@@ -113,7 +109,7 @@
</thead>
<tbody>
{% for sample in sample_type.sample_list %}
- <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}">
+ <tr class="{{ sample.class_outlier }} value_se" id="{% if outer_loop.index == 1 %}Primary_{{ sample.this_id }}{% else %}Other_{{ sample.this_id }}{% endif %}">
<td align="center" style="padding-left: 0px; padding-right: 0px;" class="column_name-"><input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" value="{{ sample.name }}" checked="checked">
</td>
<td class="column_name-Index" align="right">{{ loop.index }}</td>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 8e003897..e0bc8eb8 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -14,11 +14,6 @@
<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" %}
@@ -39,6 +34,16 @@
<div class="tab-content">
<div class="tab-pane active" id="gemma">
<div style="padding-top: 20px;" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
+ <div style="margin-left:20px;" class="col-xs-2 controls">
+ <select id="chr_gemma" class="form-control">
+ {% for item in chr_list %}
+ <option value="{{ item[1] }}">{{ item[0] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
<label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
@@ -61,11 +66,11 @@
<label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
<label class="radio-inline">
- <input type="radio" name="use_loco" value="True">
+ <input type="radio" name="use_loco" value="True" checked="">
Yes
</label>
<label class="radio-inline">
- <input type="radio" name="use_loco" value="False" checked="">
+ <input type="radio" name="use_loco" value="False">
No
</label>
</div>
@@ -110,6 +115,16 @@
{% if dataset.group.mapping_id == "1" %}
<div class="tab-pane" id="interval_mapping">
<div style="margin-top: 20px" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
+ <div style="margin-left:20px;" class="col-xs-2 controls">
+ <select id="chr_reaper" class="form-control">
+ {% for item in chr_list %}
+ <option value="{{ item[1] }}">{{ item[0] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
<label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
@@ -202,6 +217,16 @@
</div>
<div class="tab-pane" id="rqtl_geno">
<div style="margin-top: 20px" class="form-horizontal">
+ <div class="mapping_method_fields form-group">
+ <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
+ <div style="margin-left:20px;" class="col-xs-2 controls">
+ <select id="chr_rqtl_geno" class="form-control">
+ {% for item in chr_list %}
+ <option value="{{ item[1] }}">{{ item[0] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
{% if genofiles and genofiles|length>0 %}
<div class="mapping_method_fields form-group">
<label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
@@ -304,30 +329,6 @@
</div>
</div>
</div>
- <div class="tab-pane" id="pylmm">
- <div style="margin-top: 20px" class="form-horizontal">
- {% if genofiles and genofiles|length>0 %}
- <div class="mapping_method_fields form-group">
- <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
- <div style="margin-left: 20px;" class="col-xs-4 controls">
- <select id="genofile_pylmm" class="form-control">
- {% for item in genofiles %}
- <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
- {% endfor %}
- </select>
- </div>
- </div>
- {% endif %}
- <div class="mapping_method_fields form-group">
- <label class="col-xs-3 control-label"></label>
- <div style="margin-left:20px;" class="col-xs-6">
- <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
- Compute
- </button>
- </div>
- </div>
- </div>
- </div>
{% endif %}
</div>
</div>
@@ -341,10 +342,6 @@
<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>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index ac0c753a..a0bdc987 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -5,15 +5,15 @@
<a href="#stats_tab" data-toggle="tab">Basic Statistics</a>
</li>
<li>
- <a href="#histogram_tab" data-toggle="tab">Histogram</a>
+ <a href="#histogram_tab" class="histogram_tab" data-toggle="tab">Histogram</a>
</li>
{% if num_values < 256 %}
<li>
- <a href="#bar_chart_tab" data-toggle="tab">Bar Chart</a>
+ <a href="#bar_chart_tab" class="bar_chart_tab" data-toggle="tab">Bar Chart</a>
</li>
{% endif %}
<li>
- <a href="#probability_plot" data-toggle="tab">Probability Plot</a>
+ <a href="#probability_plot" class="prob_plot_tab" data-toggle="tab">Probability Plot</a>
</li>
{% if g.user_session.logged_in %}
<li>
@@ -21,10 +21,10 @@
</li>
{% endif %}
<li>
- <a href="#box_plot_tab" data-toggle="tab">Box Plot</a>
+ <a href="#box_plot_tab" class="box_plot_tab" data-toggle="tab">Box Plot</a>
</li>
<li>
- <a href="#violin_plot_tab" data-toggle="tab">Violin Plot</a>
+ <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
</li>
</ul>
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
new file mode 100644
index 00000000..5d14a30e
--- /dev/null
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -0,0 +1,79 @@
+<div>
+ <div class="form-horizontal">
+ <legend>Block samples</legend>
+ <p>Edit or delete values in the Trait Data boxes, and use the
+ <strong>Reset</strong> option as
+ needed.
+ </p>
+
+ <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
+ <label for="remove_samples_field">Block samples by index:</label>
+ <input type="text" id="remove_samples_field">
+ <select id="block_group" size="1">
+ <option value="primary">
+ {{ sample_group_types['samples_primary'] }}
+ </option>
+ <option value="other">
+ {{ sample_group_types['samples_other'] }}
+ </option>
+ </select>
+ <input type="button" id="block_by_index" class="btn" value="Block">
+ </div>
+ <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
+ Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
+ </div>
+ {% if sample_groups[0].attributes %}
+ <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
+ <label for="exclude_menu">Block samples by group:</label>
+ <select id="exclude_menu" size=1>
+ {% for attribute in sample_groups[0].attributes %}
+ <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+ {{ sample_groups[0].attributes[attribute].name }}</option>
+ {% endfor %}
+ </select>
+ <select id="attribute_values" size=1>
+ </select>
+ <input type="button" id="exclude_group" class="btn" value="Block">
+ </div>
+ {% endif %}
+ <div>
+ <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+ <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
+ <input type="button" id="reset" class="btn btn-primary" value="Reset">
+ <span class="input-append">
+ <input type="button" id="export" class="btn btn-default" value="Export">
+ <select id="export_format" class="select optional span2">
+ <option value="excel">Excel</option>
+ <option value="csv">CSV</option>
+ </select>
+ </span>
+ <br>
+ <div style="margin-top:10px;">
+ <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="qnorm">Quantile</option>
+ <option value="sqrt">Square Root</option>
+ </select>
+ </div>
+ <!--
+ {% if sample_groups[0].sample_qnorm is not none %}
+ <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+ {% endif %}
+ -->
+ </div>
+ <br>
+
+ <div>
+ <p>Outliers highlighted in
+ <strong style="background-color:yellow;">yellow</strong>
+ can be hidden using
+ the <strong>Hide Outliers</strong> button.
+ </p>
+
+ <p>Samples with no value (x) can be hidden by clicking
+ <strong>Hide No Value</strong> button.
+ </p>
+ </div>
+ </div>
+</div> \ No newline at end of file