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Adding filter for mtRNA #110

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Nov 27, 2023
Merged

Adding filter for mtRNA #110

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11 changes: 10 additions & 1 deletion src/grinch/filters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,10 +5,12 @@
import numpy as np
from anndata import AnnData
from pydantic import NonNegativeFloat, NonNegativeInt, validate_call
from sklearn.utils.validation import check_non_negative
from sklearn.utils.validation import check_non_negative, column_or_1d

from .aliases import OBS, VAR
from .base import StorageMixin
from .conf import BaseConfigurable
from .processors import ReadKey
from .utils import any_not_None, true_inside
from .utils.decorators import plt_interactive
from .utils.plotting import plot1d
Expand Down Expand Up @@ -132,6 +134,8 @@ class Config(BaseFilter.Config):
max_counts: NonNegativeFloat | None = None
min_cells: NonNegativeInt | None = None
max_cells: NonNegativeInt | None = None
remove_MT_genes: bool = False
gene_names_key: ReadKey = "var_names" # only used if remove_MT_genes

cfg: Config

Expand Down Expand Up @@ -170,6 +174,11 @@ def _filter(self, adata: AnnData) -> None:
self.cfg.max_cells,
)

if self.cfg.remove_MT_genes:
gene_names = StorageMixin.read(adata, self.cfg.gene_names_key)
gene_names = np.char.upper(column_or_1d(gene_names).astype(str))
to_keep &= ~np.char.startswith(gene_names, 'MT-')

if to_keep.sum() < 1:
raise ValueError(
"Filtering options are too stringent. "
Expand Down
21 changes: 21 additions & 0 deletions tests/test_filters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -235,11 +235,13 @@ def test_gene_all(X):
"min_counts": 6,
"min_cells": 1,
"max_cells": 2,
"remove_MT_genes": True,
}
)
cfg = instantiate(cfg)
filter_genes = cfg.create()
adata = AnnData(X)
adata.var_names = ["G1", "MT2", "MT-3", "G4"]
X_original = adata.X.copy()
filter_genes(adata)
assert_allclose(X_original, X)
Expand All @@ -249,6 +251,25 @@ def test_gene_all(X):
assert_allclose(adata.var[VAR.N_CELLS], [2])


@pytest.mark.parametrize("X", X_mods)
def test_gene_MT(X):
cfg = OmegaConf.create(
{
"_target_": "src.grinch.FilterGenes.Config",
"remove_MT_genes": True,
}
)
cfg = instantiate(cfg)
filter_genes = cfg.create()
adata = AnnData(X)
adata.var_names = ["G1", "MT2", "MT-3", "G4"]
X_original = adata.X.copy()
filter_genes(adata)
assert_allclose(X_original, X)
X_filtered = X[:, [0, 1, 3]]
assert_allclose(X_filtered, adata.X)


@pytest.mark.parametrize("X", X_mods)
def test_gene_inplace(X):
cfg = OmegaConf.create(
Expand Down