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authorzsloan2016-04-06 19:36:53 +0000
committerzsloan2016-04-06 19:36:53 +0000
commit42f465b7327090d3e648c69c73b3cc3e0f452a6f (patch)
tree675630604c59ef943619af07116f80b14762b3ab /wqflask
parentb1e0067c95efa7d2fffa0dd1230b917121869709 (diff)
downloadgenenetwork2-42f465b7327090d3e648c69c73b3cc3e0f452a6f.tar.gz
Setting lodm to always be 1.0 fixes the issue where it would incorrectly display LOD scores for the Y-Axis instead of LRS values
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py16
1 files changed, 9 insertions, 7 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index b8307aaa..692e381b 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1869,17 +1869,19 @@ class MarkerRegression(object):
#LRSTop is then defined to be above the LRSMax by enough to add one additional LRSScale increment.
#if we are using a set-scale, then we set LRSTop to be the user's value, and LRSMax doesn't matter.
- if self.LRS_LOD == 'LRS':
- lodm = self.LODFACTOR
- else:
- lodm = 1.0
+ #ZS: I'm not sure what this if statement is supposed to do. It appears to work correctly for both LOD and LRS if I just set lodm to 1.0
+ #if self.LRS_LOD == 'LRS':
+ # lodm = self.LODFACTOR
+ #else:
+ # lodm = 1.0
+ lodm = 1.0
if self.lrsMax <= 0: #sliding scale
- if "lod_score" in self.qtlresults[0]:
- LRSMax = max([result['lod_score'] for result in self.qtlresults])
+ if self.LRS_LOD == "LRS" and "lrs_value" in self.qtlresults[0]:
+ LRSMax = max([result['lrs_value'] for result in self.qtlresults])
#LRSMax = max(map(max, self.qtlresults)).lrs_value
else:
- LRSMax = max([result['lrs_value'] for result in self.qtlresults])
+ LRSMax = max([result['lod_score'] for result in self.qtlresults])
#LRSMax = max(map(max, self.qtlresults)).lod_score
#genotype trait will give infinite LRS
LRSMax = min(LRSMax, webqtlConfig.MAXLRS)