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-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py2
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py8
-rw-r--r--wqflask/wqflask/templates/correlation_page.html33
3 files changed, 22 insertions, 21 deletions
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 51aa1622..0c1cea0e 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -498,7 +498,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
if bool(trait.description_display):
results_dict['description'] = trait.description_display
if bool(trait.mean):
- results_dict['mean'] = float(trait.mean)
+ results_dict['mean'] = f"{float(trait.mean):.3f}"
if trait.LRS_score_repr != "N/A":
results_dict['lrs_score'] = f"{float(trait.LRS_score_repr):.1f}"
results_dict['lrs_location'] = trait.LRS_location_repr
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 02f91a32..61e4897c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -31,7 +31,8 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
this_chromosomes = this_dataset.species.chromosomes.chromosomes
- this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes]
+ this_chromosomes_name=[this_chromosomes[chromosome].name for chromosome in this_chromosomes]
+
chr_list_string=",".join(this_chromosomes_name)
if covariates != "":
@@ -45,7 +46,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
genofile_name,
TEMPDIR,
k_output_filename)
- logger.debug("k_command:" + generate_k_command)
+
os.system(generate_k_command)
gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
@@ -77,7 +78,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
k_output_filename)
- logger.debug("k_command:" + generate_k_command)
os.system(generate_k_command)
gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
@@ -93,8 +93,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
else:
gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename)
-
- logger.debug("gemma_command:" + gemma_command)
os.system(gemma_command)
else:
gwa_output_filename = output_files
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index aa74abf5..06ee9056 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -80,19 +80,21 @@
<input type="hidden" name="database_name" id="database_name" value="None">
<input type="hidden" name="export_data" id="export_data" value="">
<input type="hidden" name="file_name" id="file_name" value="{{ this_trait.name }}_{{ dataset.name }}_correlation">
- <button class="btn btn-default" id="export_traits">Download CSV</button>
<input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search Table For ...">
<input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
<button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
<button id="redraw" class="btn btn-default" type="button">Reset Columns</button>
</form>
<br />
+ <div id="export_options"></div>
{% if target_dataset.type != "Publish" %}
<br />
- <button id="more_options" class="btn btn-primary">More Options...</button>
+ <div style="float: left; clear: left; margin-top: 10px; margin-bottom: 20px;">
+ <button id="more_options" class="btn btn-primary">More Options...</button>
+ </div>
<br />
<br />
- <div id="filter_options" style="display: none;">
+ <div id="filter_options" style="display: none; float: left; clear: left;">
<span style="border: 1px dashed #999999; padding: 8px; background-color: #ddf; font-size: 12px;">
<button id="select_traits" class="btn btn-primary" style="font-size: 12px; padding: 2px 3px;">Select Traits</button> with r >
<input type="text" name="r_greater_select" value="-1.0" size="6" maxlength="10">
@@ -115,7 +117,7 @@
</div>
{% endif %}
</div>
- <div class="show-hide-container">
+ <div class="show-hide-container" style="float: left; clear: left;">
<b>Show/Hide Columns:</b>
<br>
<button class="toggle-vis" data-column="1">Index</button>
@@ -174,7 +176,7 @@
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.html5.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
<script language="javascript" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.1/js/all.min.js"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/scroller/2.0.2/js/dataTables.scroller.min.js"></script>
@@ -259,17 +261,14 @@
$(document).ready( function () {
table_conf = {
buttons: [
- {
- extend: 'columnsToggle',
- columns: function( idx, data, node ) {
- if (idx != 0) {
- return true;
- } else {
- return false;
- }
- },
- postfixButtons: [ 'colvisRestore' ]
+ {
+ extend: 'csvHtml5',
+ text: 'Download <span class="glyphicon glyphicon-download"></span>',
+ className: 'btn btn-default',
+ exportOptions: {
+ columns: 'th:not(:first-child)'
}
+ }
],
'drawCallback': function( settings ) {
$('#trait_table tr').off().on("click", function(event) {
@@ -544,6 +543,10 @@
trait_table = $('#trait_table').DataTable(table_conf);
+ trait_table.buttons().container().appendTo('#export_options')
+
+ $('.buttons-csv').removeClass('dt-button')
+
trait_table.on( 'order.dt search.dt draw.dt', function () {
trait_table.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) {
cell.innerHTML = i+1;