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authorzsloan2016-04-14 21:19:12 +0000
committerzsloan2016-04-14 21:19:12 +0000
commitbe3c688ac3ddcc4f10a359bf68792e05dca63973 (patch)
treeef6c9d499b6e1f07fb9d00681988f6a388e174e2
parent15b3a1543f59a097039ae964ba26775236022401 (diff)
downloadgenenetwork2-be3c688ac3ddcc4f10a359bf68792e05dca63973.tar.gz
Fixed issue where qtl lines in interval mapping wouldn't connect between chromosomes
Added text explaining what * indicates in the mapping options menu Removed ranges (log2 and fold) from stats table for phenotype traits
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py8
-rwxr-xr-xwqflask/wqflask/search_results.py4
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py9
-rw-r--r--[-rwxr-xr-x]wqflask/wqflask/static/new/javascript/show_trait.js3
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html9
-rwxr-xr-xwqflask/wqflask/templates/show_trait_statistics.html1
6 files changed, 19 insertions, 15 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 63f62411..c10aac73 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -2015,6 +2015,9 @@ class MarkerRegression(object):
thisLRSColor = self.colorCollection[0]
if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
+ if self.manhattan_plot != True:
+ canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
+ LRSCoordXY = []
previous_chr = qtlresult['chr']
previous_chr_as_int += 1
@@ -2032,7 +2035,6 @@ class MarkerRegression(object):
else:
this_chr = str(self.ChrList[self.selectedChr][1]+1)
if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
- #LRSCoordXY = []
#AdditiveCoordXY = []
#DominanceCoordXY = []
#for k, _locus in enumerate(_chr):
@@ -2087,7 +2089,6 @@ class MarkerRegression(object):
# Yc = yZero - qtlresult['dominance']*DominanceHeightThresh/dominanceMax
# DominanceCoordXY.append((Xc, Yc))
m += 1
-
#canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
lineWidth = 1
@@ -2151,9 +2152,6 @@ class MarkerRegression(object):
canvas.drawLine(Xc0, yZero - (Yc0-yZero), Xc, yZero - (Yc-yZero), color=minusColor, width=lineWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
- if self.manhattan_plot != True:
- canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
-
###draw additive scale
if not self.multipleInterval and self.additiveChecked:
additiveScaleFont=pid.Font(ttf="verdana",size=16*zoom,bold=0)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fb03f027..a57bfffe 100755
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -119,9 +119,9 @@ class SearchResultPage(object):
#### Excel file needs to be generated ####
- print("foo locals are:", locals())
+ #print("foo locals are:", locals())
trait_id = result[0]
- this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True)
+ this_trait = GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
self.trait_list.append(this_trait)
self.dataset.get_trait_info(self.trait_list, species)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 3cc6121f..2d4c952a 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -152,10 +152,11 @@ class ShowTrait(object):
self.trait_table_width = get_trait_table_width(self.sample_groups)
- js_data = dict(sample_group_types = self.sample_group_types,
- sample_lists = sample_lists,
- attribute_names = self.sample_groups[0].attributes,
- temp_uuid = self.temp_uuid)
+ js_data = dict(dataset_type = self.dataset.type,
+ sample_group_types = self.sample_group_types,
+ sample_lists = sample_lists,
+ attribute_names = self.sample_groups[0].attributes,
+ temp_uuid = self.temp_uuid)
self.js_data = js_data
def get_mapping_methods(self):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 8d5982b7..663f7f3b 100755..100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -186,6 +186,9 @@
the_rows = "<tbody>";
for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
row = Stat_Table_Rows[_i];
+ if ((row.vn == "range_fold" || row.vn == "range") && js_data.dataset_type == "Publish"){
+ continue;
+ }
console.log("rowing");
row_line = "<tr>";
if (row.url != null) {
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index d7950754..c65948c0 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -87,8 +87,8 @@
</td>
</tr>
</table>
- </div>
- <div class="col-xs-4" style="padding: 0px;">
+ </div>
+ <div class="col-xs-4" style="padding: 0px;">
{% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %}
<input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test
<a href="http://genenetwork.org/glossary.html#Permutation" target="_blank">
@@ -121,7 +121,10 @@
{% if plotScale != "morgan" %}
<input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span>
{% endif %}
- </div>
+ </div>
+ <div class="col-xs-12" align="center" style="padding: 5px;">
+ <span style="color:red;">*</span> <span style="font-size: 12px;">only apply to single chromosome physical mapping</span>
+ </div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 2183dd30..9c5c94b2 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -27,7 +27,6 @@
<div class="tab-pane active" id="stats_tab">
<div style="padding: 20px" class="form-horizontal">
<table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table>
-
</div>
</div>
<div class="tab-pane" id="histogram_tab">