From d6227b9e0a331b2cb3db705a503dcfa5bbaf1555 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Nov 2020 13:42:18 -0600
Subject: Substituted -log(p) with -logP as mentioned in Rob's e-mail

---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 6 +++---
 wqflask/wqflask/marker_regression/run_mapping.py             | 8 ++++----
 wqflask/wqflask/templates/mapping_results.html               | 8 ++++----
 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 %}
-- 
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