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From: Kevin Murray <kdmfoss@gmail.com>
Date: Thu, 22 Dec 2016 20:07:13 +1100
Subject: Cherry-pick upstream fix for numpy transition
---
skbio/stats/composition.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/skbio/stats/composition.py b/skbio/stats/composition.py
index eb6b364..95f7820 100644
--- a/skbio/stats/composition.py
+++ b/skbio/stats/composition.py
@@ -973,8 +973,8 @@ def ancom(table, grouping,
# Multiple comparisons
if multiple_comparisons_correction == 'holm-bonferroni':
- logratio_mat = np.apply_along_axis(_holm_bonferroni,
- 1, logratio_mat)
+ logratio_mat = np.vstack([_holm_bonferroni(logratio_mat[i, :])
+ for i in range(logratio_mat.shape[0])])
np.fill_diagonal(logratio_mat, 1)
W = (logratio_mat < alpha).sum(axis=1)
c_start = W.max() / n_feat
@@ -1079,9 +1079,8 @@ def _log_compare(mat, cats,
for i in range(c-1):
ratio = (log_mat[:, i].T - log_mat[:, i+1:].T).T
- m, p = np.apply_along_axis(func,
- axis=0,
- arr=ratio)
+ p = np.array([func(ratio[:, i])[1]
+ for i in range(ratio.shape[1])])
log_ratio[i, i+1:] = np.squeeze(np.array(p.T))
return log_ratio
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