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authorzsloan2016-08-03 16:35:13 +0000
committerzsloan2016-08-03 16:35:13 +0000
commit08849a27af933340fc14decf8dfdd62e3d65b3b3 (patch)
tree440546f932c06c1660611c8fbb9d8e86c3233481
parentc33d090f2067c19ea1229dad1e6b45cdb57c0612 (diff)
downloadgenenetwork2-08849a27af933340fc14decf8dfdd62e3d65b3b3.tar.gz
Fixed issue with certain sample names (for example BXD48a, BXD72a, etc) that caused single chromosome mapping to not work
Disabled bootstrap for mapping unil issue causing wrong results is fixed Added header to first column of basic statistics table and increased width to avoid rows spilling over to second line
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression.py4
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py5
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js2
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html2
5 files changed, 9 insertions, 6 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 510b26af..a8324442 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -57,7 +57,9 @@ class MarkerRegression(object):
self.samples = [] # Want only ones with values
self.vals = []
- #for sample in self.this_trait.data.keys():
+ all_samples_ordered = self.dataset.group.all_samples_ordered()
+ primary_sample_names = list(all_samples_ordered)
+
for sample in self.dataset.group.samplelist:
in_trait_data = False
for item in self.this_trait.data:
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9573a9de..d0509c75 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -169,6 +169,7 @@ class MarkerRegression(object):
self.species = start_vars['species']
#Needing for form submission when doing single chr mapping or remapping after changing options
+ self.samples = start_vars['samples']
self.vals = start_vars['vals']
self.mapping_method = start_vars['mapping_method']
if self.mapping_method == "rqtl_geno":
@@ -801,8 +802,8 @@ class MarkerRegression(object):
plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
#draw bootstap
- if self.bootChecked and not self.multipleInterval:
- self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset)
+ #if self.bootChecked and not self.multipleInterval:
+ # self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset)
# Draw clickable region and gene band if selected
if self.plotScale == 'physic' and self.selectedChr > -1:
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 419aa7a2..feaaac30 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -173,7 +173,7 @@
};
make_table = function() {
var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
- header = "<thead><tr><th>&nbsp;</th>";
+ header = "<thead><tr><th>Statistic</th>";
_ref = js_data.sample_group_types;
for (key in _ref) {
if (!__hasProp.call(_ref, key)) continue;
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 978ea55f..5389978a 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -15,7 +15,7 @@
<input type="hidden" name="trait_id" value="{{ this_trait.name }}">
<input type="hidden" name="dataset" value="{{ dataset.name }}">
<input type="hidden" name="method" value="{{ mapping_method }}">
- {% for sample in dataset.group.samplelist %}
+ {% for sample in samples %}
<input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
{% endfor %}
<input type="hidden" name="maf">
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 3ee8bdea..62d6dcfd 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -26,7 +26,7 @@
<div class="tab-content">
<div class="tab-pane active" id="stats_tab">
<div style="padding: 20px" class="form-horizontal">
- <table border="1" id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped cell-border"></table>
+ <table border="1" id="stats_table" style="width: 450px; float: left;" class="table table-hover table-striped cell-border"></table>
</div>
</div>
<div class="tab-pane" id="histogram_tab">