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authorzsloan2020-11-12 13:42:18 -0600
committerzsloan2020-11-12 13:42:18 -0600
commitd6227b9e0a331b2cb3db705a503dcfa5bbaf1555 (patch)
tree0b880b3fd0ae81e4c6488aae386918a7aafd4446 /wqflask
parent6feb7dd0f8020c7ed54b70be6a15c099dc62b490 (diff)
downloadgenenetwork2-d6227b9e0a331b2cb3db705a503dcfa5bbaf1555.tar.gz
Substituted -log(p) with -logP as mentioned in Rob's e-mail
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py6
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py8
-rw-r--r--wqflask/wqflask/templates/mapping_results.html8
3 files changed, 11 insertions, 11 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 6d6572ff..3f6de2b2 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2076,7 +2076,7 @@ class DisplayMappingResults(object):
if self.lrsMax <= 0: #sliding scale
if "lrs_value" in self.qtlresults[0]:
LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults])
- if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)":
+ if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS)
@@ -2172,7 +2172,7 @@ class DisplayMappingResults(object):
TEXT_X_DISPLACEMENT = -12
else:
TEXT_X_DISPLACEMENT = -30
- if self.LRS_LOD == "-log(p)":
+ if self.LRS_LOD == "-logP":
TEXT_Y_DISPLACEMENT = -242
else:
TEXT_Y_DISPLACEMENT = -210
@@ -2397,7 +2397,7 @@ class DisplayMappingResults(object):
if 'lrs_value' in qtlresult:
- if self.LRS_LOD == "LOD" or self.LRS_LOD == "-log(p)":
+ if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 9625349c..31d6a67c 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -228,7 +228,7 @@ class RunMapping(object):
self.output_files = start_vars['output_files']
if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
self.first_run = False
- self.score_type = "-log(p)"
+ self.score_type = "-logP"
self.manhattan_plot = True
with Bench("Running GEMMA"):
if self.use_loco == "True":
@@ -327,7 +327,7 @@ class RunMapping(object):
self.control_marker,
self.manhattan_plot)
elif self.mapping_method == "plink":
- self.score_type = "-log(p)"
+ self.score_type = "-logP"
self.manhattan_plot = True
results = plink_mapping.run_plink(self.this_trait, self.dataset, self.species, self.vals, self.maf)
#results = self.run_plink()
@@ -539,8 +539,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n")
output_file.write("\n")
output_file.write("Name,Chr,")
- if score_type.lower() == "-log(p)":
- score_type = "-log(p)"
+ if score_type.lower() == "-logP":
+ score_type = "-logP"
if 'Mb' in markers[0]:
output_file.write("Mb," + score_type)
if 'cM' in markers[0]:
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index e68a792a..28d93542 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -99,7 +99,7 @@
<input type="radio" name="LRSCheck" value="LRS" {% if LRS_LOD == "LRS" %}checked{% endif %}>LRS
</label>
<label class="radio-inline">
- <input type="radio" name="LRSCheck" value="{% if LRS_LOD == "-log(p)" %}-log(p){% else %}LOD{% endif %}" {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}checked{% endif %}>{% if LRS_LOD == "-log(p)" %}-log(p){% else %}LOD{% endif %}
+ <input type="radio" name="LRSCheck" value="{% if LRS_LOD == "-logP" %}-logP{% else %}LOD{% endif %}" {% if LRS_LOD == "LOD" or LRS_LOD == "-logP" %}checked{% endif %}>{% if LRS_LOD == "-logP" %}-logP{% else %}LOD{% endif %}
</label>
<a href="http://genenetwork.org/glossary.html#LOD" target="_blank">
<sup style="color:#f00"> ?</sup>
@@ -235,8 +235,8 @@
<th></th>
<th>Row</th>
<th>Marker</th>
- {% if LRS_LOD == "-log(p)" %}
- <th><div style="text-align: right;">–log(p)</div></th>
+ {% if LRS_LOD == "-logP" %}
+ <th><div style="text-align: right;">–logP</div></th>
{% else %}
<th><div style="text-align: right;">{{ LRS_LOD }}</div></th>
{% endif %}
@@ -259,7 +259,7 @@
</td>
<td align="right">{{ loop.index }}</td>
<td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
- {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
+ {% if LRS_LOD == "LOD" or LRS_LOD == "-logP" %}
{% if 'lod_score' in marker %}
<td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
{% else %}