File size: 2,200 Bytes
9d901ad | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | """Tests for the preprocessing module."""
import numpy as np
import pytest
from scipy.sparse import issparse
def test_filter_genes(synthetic_adata):
import scptr
n_before = synthetic_adata.n_vars
scptr.pp.filter_genes(
synthetic_adata, min_unspliced_counts=10, min_unspliced_cells=10
)
assert synthetic_adata.n_vars <= n_before
assert synthetic_adata.n_vars > 0
assert "filter_genes" in synthetic_adata.uns["scptr"]
def test_filter_cells(synthetic_adata):
import scptr
n_before = synthetic_adata.n_obs
scptr.pp.filter_cells(synthetic_adata, min_unspliced_counts=1)
assert synthetic_adata.n_obs <= n_before
assert synthetic_adata.n_obs > 0
def test_normalize_layers(synthetic_adata):
import scptr
scptr.pp.normalize_layers(synthetic_adata)
# After normalization, layers should be dense float32
assert not issparse(synthetic_adata.layers["spliced"])
assert synthetic_adata.layers["spliced"].dtype == np.float32
assert not issparse(synthetic_adata.layers["unspliced"])
assert "normalize_layers" in synthetic_adata.uns["scptr"]
def test_neighbors(synthetic_adata):
import scptr
scptr.pp.normalize_layers(synthetic_adata)
scptr.pp.neighbors(synthetic_adata, n_neighbors=10)
assert "distances" in synthetic_adata.obsp
assert "connectivities" in synthetic_adata.obsp
assert "neighbors" in synthetic_adata.uns["scptr"]
def test_smooth_layers(synthetic_adata):
import scptr
scptr.pp.normalize_layers(synthetic_adata)
scptr.pp.neighbors(synthetic_adata, n_neighbors=10)
scptr.pp.smooth_layers(synthetic_adata)
assert "Mu" in synthetic_adata.layers
assert "Ms" in synthetic_adata.layers
assert synthetic_adata.layers["Mu"].shape == synthetic_adata.shape
assert synthetic_adata.layers["Ms"].shape == synthetic_adata.shape
assert synthetic_adata.layers["Mu"].dtype == np.float32
def test_smooth_fixed_bandwidth(synthetic_adata):
import scptr
scptr.pp.normalize_layers(synthetic_adata)
scptr.pp.neighbors(synthetic_adata, n_neighbors=10)
scptr.pp.smooth_layers(synthetic_adata, bandwidth=1.0)
assert "Mu" in synthetic_adata.layers
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