From 63ca33f75fcb67ba8c3851c60088b62becb5f735 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 27 Apr 2021 22:25:44 +0000
Subject: Convert to array and transpose R/qtl scanone results when not using
 cofactors. For some reason the rows/columns are inverted when converted to a
 python object when doing scanone with cofactors vs without cofactors

---
 wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c70fbbec..cd43577e 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -116,7 +116,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
             result_data_frame = ro.r("qtl_results")
         else:
             ro.r(f"qtl_results = scanone(the_cross, pheno='the_pheno', model='{model}', method='{method}')")
-            result_data_frame = ro.r("qtl_results")
+            result_data_frame = np.asarray(ro.r("qtl_results")).T
 
         marker_names = np.asarray(ro.r("row.names(qtl_results)"))
         if num_perm > 0 and permCheck == "ON":                                                                   # Do permutation (if requested by user)
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