From a37bc6e233d49fecd81f7ec3d3f5527c77de12c4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 Mar 2019 11:46:55 -0600
Subject: Fixed issue where correlation results containing NaN results sorted
 incorrectly

Set default permutations for R/qtl to 200
---
 wqflask/wqflask/correlation/show_corr_results.py        | 7 +++++--
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 0b2875cc..c15c3579 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -33,6 +33,7 @@ import resource
 import json
 
 import scipy
+import numpy
 
 from pprint import pformat as pf
 
@@ -175,7 +176,6 @@ class CorrelationResults(object):
             self.correlation_data = collections.OrderedDict(sorted(self.correlation_data.items(),
                                                                    key=lambda t: -abs(t[1][0])))
 
-
             if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
                 #ZS: Convert min/max chromosome to an int for the location range option
                 range_chr_as_int = None
@@ -456,7 +456,10 @@ class CorrelationResults(object):
             sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals)
 
         if num_overlap > 5:
-            self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
+            if numpy.isnan(sample_r):
+                pass
+            else:
+                self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
 
     def process_samples(self, start_vars, sample_names, excluded_samples=None):
         if not excluded_samples:
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c7fd2612..b5ed1c8f 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -242,7 +242,7 @@
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
-                                <input name="num_perm_rqtl_geno" value="0" type="text" class="form-control">
+                                <input name="num_perm_rqtl_geno" value="200" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
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