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authorzsloan2015-09-01 16:33:22 +0000
committerzsloan2015-09-01 16:33:22 +0000
commit99f56231b94583a64410a57b842f1d910c4e3f2e (patch)
tree3d3b43410389a2710e66c808c79eb0ba4c3b002e /wqflask
parent08b87bbd353f0041a820ba0d02a1348c244b5e3b (diff)
downloadgenenetwork2-99f56231b94583a64410a57b842f1d910c4e3f2e.tar.gz
Fixed issue that caused R/qtl mapping to not work
Removed bootstrap and additive effect options until I can get them working correctly
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py9
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py6
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html7
3 files changed, 13 insertions, 9 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 108bc747..46aac86c 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -92,10 +92,11 @@ class IntervalMapping(object):
self.manhattan_plot = True
else:
self.manhattan_plot = False
- if start_vars['display_additive'] == "yes":
- self.additive = True
- else:
- self.additive = False
+ #ZS: Commenting this out until we can fix the issue with positive/negative additive effects being colored properly
+ #if start_vars['display_additive'] == "yes":
+ # self.additive = True
+ #else:
+ self.additive = False
if 'control_locus' in start_vars:
self.control_locus = start_vars['control_locus']
else:
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1c5757a6..757aeb72 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -73,9 +73,11 @@ class MarkerRegression(object):
self.suggestive = ""
self.significant = ""
self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
+ self.score_type = "LRS" #ZS: LRS or LOD
self.dataset.group.get_markers()
if self.mapping_method == "gemma":
+ self.score_type = "LOD"
included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
self.dataset.group.get_specified_markers(markers = included_markers)
self.dataset.group.markers.add_pvalues(p_values)
@@ -83,6 +85,7 @@ class MarkerRegression(object):
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
+ self.score_type = "LOD"
if start_vars['num_perm'] == "":
self.num_perm = 0
else:
@@ -136,7 +139,6 @@ class MarkerRegression(object):
)
else:
- self.score_type = "LRS"
self.cutoff = 2
self.qtl_results = []
highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
@@ -165,7 +167,7 @@ class MarkerRegression(object):
else:
self.json_data['chr'].append(str(qtl['chr']))
self.json_data['pos'].append(qtl['Mb'])
- if self.score_type == "LRS":
+ if 'lrs_value' in qtl:
self.json_data['lod.hk'].append(str(qtl['lrs_value']))
else:
self.json_data['lod.hk'].append(str(qtl['lod_score']))
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index b9ac80bf..7f26a252 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -9,7 +9,7 @@
<a href="#pylmm" data-toggle="tab">pyLMM</a>
</li>
<li>
- <a href="#rqtl_geno" data-toggle="tab">rqtl</a>
+ <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
</li>
<li>
<a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
@@ -169,14 +169,14 @@
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
-
+<!--
<div class="mapping_method_fields form-group">
<label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="mapping_bootstraps" value="2000" type="text" class="form-control">
</div>
</div>
-
+
<div class="mapping_method_fields form-group">
<label style="text-align:left;" class="col-xs-12 control-label">Display Additive Effect</label>
<div class="col-xs-12 controls" id="display_additive_effect">
@@ -190,6 +190,7 @@
</label>
</div>
</div>
+-->
<div class="mapping_method_fields form-group">
<label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>