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Added smillie_2019 dataloader and renamed smillie dataset to tasccoda_example #450

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Nov 30, 2023
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Added smillie_2019 dataloader and renamed smillie dataset to tasccoda_example #450

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103c53e
Added smillie_2019 dataloader and renamed smillie to tasccoda_example
Lilly-May Nov 30, 2023
fd11536
Update pertpy/data/_datasets.py
Lilly-May Nov 30, 2023
11a8cda
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Nov 30, 2023
df9fdcd
Fixed docs explanation for tasccoda_example
Lilly-May Nov 30, 2023
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3 changes: 2 additions & 1 deletion pertpy/data/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,12 @@
schraivogel_2020_tap_screen_chr11,
sciplex3_raw,
shifrut_2018,
smillie,
smillie_2019,
srivatsan_2020_sciplex2,
srivatsan_2020_sciplex3,
srivatsan_2020_sciplex4,
stephenson_2021_subsampled,
tasccoda_example,
tian_2019_day7neuron,
tian_2019_ipsc,
tian_2021_crispra,
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36 changes: 33 additions & 3 deletions pertpy/data/_datasets.py
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Expand Up @@ -133,8 +133,12 @@ def sciplex3_raw() -> AnnData: # pragma: no cover
return adata


def smillie() -> AnnData: # pragma: no cover
"""scRNA-seq data of the small intestine of mice under Ulcerative Colitis.
def tasccoda_example() -> AnnData: # pragma: no cover
"""Example for the coda part of a mudata object.

Resulting AnnData object (mudata['coda']) when preparing a dataset for processing with tascCODA.
Created using the smillie dataset, which comprises scRNA-seq data of the small intestine of mice under Ulcerative Colitis.
The full dataset containing the actual count data can be obtained via smillie_2019().

References:
Smillie, Christopher S et al. “Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.”
Expand All @@ -143,7 +147,7 @@ def smillie() -> AnnData: # pragma: no cover
Returns:
:class:`~anndata.AnnData` object of the dataset.
"""
output_file_name = "smillie.h5ad"
output_file_name = "tasccoda_smillie.h5ad"
output_file_path = settings.datasetdir.__str__() + "/" + output_file_name
if not Path(output_file_path).exists():
_download(
Expand Down Expand Up @@ -1460,3 +1464,29 @@ def dong_2023() -> AnnData: # pragma: no cover
adata = sc.read_h5ad(output_file_path)

return adata


def smillie_2019() -> AnnData: # pragma: no cover
"""scRNA-seq data of the small intestine of mice under Ulcerative Colitis.
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The resulting AnnData when preparing this dataset for processing with tascCODA is available via tasccoda_example().

References:
Smillie, Christopher S et al. “Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.”
Cell vol. 178,3 (2019): 714-730.e22. doi:10.1016/j.cell.2019.06.029

Returns:
:class:`~anndata.AnnData` object of the dataset.
"""
output_file_name = "smillie_2019.h5ad.zip"
output_file_path = settings.datasetdir.__str__() + "/" + output_file_name.replace(".zip", "")
if not Path(output_file_path).exists():
_download(
url="https://figshare.com/ndownloader/files/43317285",
output_file_name=output_file_name,
output_path=settings.datasetdir,
is_zip=True,
)
adata = sc.read_h5ad(output_file_path)

return adata
4 changes: 2 additions & 2 deletions pertpy/plot/_coda.py
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Expand Up @@ -726,7 +726,7 @@ def draw_tree( # pragma: no cover
Examples:
Example with tascCODA:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand Down Expand Up @@ -815,7 +815,7 @@ def draw_effects( # pragma: no cover
Examples:
Example with tascCODA:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
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2 changes: 1 addition & 1 deletion pertpy/tools/_coda/_base_coda.py
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Expand Up @@ -1005,7 +1005,7 @@ def get_node_df(self, data: AnnData | MuData, modality_key: str = "coda"):
Examples:
Example with tascCODA (works only for model of type tree_agg, i.e. a tascCODA model):
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
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16 changes: 8 additions & 8 deletions pertpy/tools/_coda/_tasccoda.py
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Expand Up @@ -104,7 +104,7 @@ def load(

Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand Down Expand Up @@ -176,7 +176,7 @@ def prepare(

Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand Down Expand Up @@ -322,7 +322,7 @@ def set_init_mcmc_states(self, rng_key: None, ref_index: np.ndarray, sample_adat

Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand Down Expand Up @@ -486,7 +486,7 @@ def make_arviz( # type: ignore

Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand Down Expand Up @@ -597,7 +597,7 @@ def run_nuts(
"""
Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand All @@ -617,7 +617,7 @@ def summary(self, data: AnnData | MuData, extended: bool = False, modality_key:
"""
Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand All @@ -638,7 +638,7 @@ def credible_effects(self, data: AnnData | MuData, modality_key: str = "coda", e
"""
Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand All @@ -659,7 +659,7 @@ def set_fdr(self, data: AnnData | MuData, est_fdr: float, modality_key: str = "c
"""
Examples:
>>> import pertpy as pt
>>> adata = pt.dt.smillie()
>>> adata = pt.dt.tasccoda_example()
>>> tasccoda = pt.tl.Tasccoda()
>>> mdata = tasccoda.load(
>>> adata, type="sample_level",
Expand Down
2 changes: 1 addition & 1 deletion tests/tools/_coda/test_tasccoda.py
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Expand Up @@ -20,7 +20,7 @@ class TesttascCODA:

@pytest.fixture
def smillie_adata(self):
smillie_adata = pt.dt.smillie()
smillie_adata = pt.dt.tasccoda_example()
smillie_adata = sc.pp.subsample(smillie_adata, 0.1, copy=True)

return smillie_adata
Expand Down
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