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Black -- formatter for python (#508)

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* Add black

* use black to format code

* Black version
This commit is contained in:
Charlotte Weaver
2018-12-12 09:44:47 -08:00
committed by GitHub
parent a847951658
commit 83154577e4
18 changed files with 636 additions and 791 deletions
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server/app/scanpy_engine/diffexp.py
+5 -9
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@@ -1,4 +1,3 @@
import numpy as np
from scipy import sparse, stats
@@ -64,19 +63,19 @@ def diffexp_ttest(adata, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
sum_vn = vnA + vnB
# degrees of freedom for Welch's t-test
with np.errstate(divide='ignore', invalid='ignore'):
dof = sum_vn**2 / (vnA**2 / (nA - 1) + vnB**2 / (nB - 1))
with np.errstate(divide="ignore", invalid="ignore"):
dof = sum_vn ** 2 / (vnA ** 2 / (nA - 1) + vnB ** 2 / (nB - 1))
dof[np.isnan(dof)] = 1
# Welch's t-test score calculation
with np.errstate(divide='ignore', invalid='ignore'):
with np.errstate(divide="ignore", invalid="ignore"):
tscores = (meanA - meanB) / np.sqrt(sum_vn)
tscores[np.isnan(tscores)] = 0
# p-value
pvals = stats.t.sf(np.abs(tscores), dof) * 2
pvals_adj = pvals * adata._X.shape[1]
pvals_adj[pvals_adj > 1] = 1 # cap adjusted p-value at 1
pvals_adj[pvals_adj > 1] = 1 # cap adjusted p-value at 1
# logfoldchanges: log2(meanA / meanB)
logfoldchanges = np.log2(np.abs((meanA + 1e-9) / (meanB + 1e-9)))
@@ -106,8 +105,5 @@ def diffexp_ttest(adata, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01):
pvals_adj_top_n = pvals_adj[sort_order]
# varIndex, logfoldchange, pval, pval_adj
result = [[sort_order[i],
logfoldchanges_top_n[i],
pvals_top_n[i],
pvals_adj_top_n[i]] for i in range(top_n)]
result = [[sort_order[i], logfoldchanges_top_n[i], pvals_top_n[i], pvals_adj_top_n[i]] for i in range(top_n)]
return result