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| author | zsloan | 2019-03-07 11:46:55 -0600 |
|---|---|---|
| committer | zsloan | 2019-03-07 11:46:55 -0600 |
| commit | a37bc6e233d49fecd81f7ec3d3f5527c77de12c4 (patch) | |
| tree | 13ff0c942ca23db0db5ff449551fc81618e538d2 | |
| parent | 92b587824a5d2bc42aab3f4be64f76113e5334eb (diff) | |
| download | genenetwork2-a37bc6e233d49fecd81f7ec3d3f5527c77de12c4.tar.gz | |
Fixed issue where correlation results containing NaN results sorted incorrectly
Set default permutations for R/qtl to 200
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 7 | ||||
| -rw-r--r-- | 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"> |