real_multi_modality #459
real_multi_modality #459
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| @@ -270,6 +274,72 @@ def _load_raw_data(self, ct_col: str = "Cell_type") -> Tuple[ad.AnnData, List[Se | |||
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| return adata, labels, idx_to_label, train_size, 0 | |||
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| def _load_raw_data_single_h5ad(self, | |||
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Get train, valid and test data through a single h5ad
| @@ -793,6 +794,14 @@ def _params_search_space(self) -> Dict[str, Dict[str, Optional[Union[str, float] | |||
| def wandb_sweep_config(self) -> Dict[str, Any]: | |||
| if self.wandb_config is None: | |||
| raise ValueError("wandb config not specified in the raw config.") | |||
| if "run_kwargs" in self.config: | |||
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Get specific run_kwargs to search
| @@ -33,7 +33,7 @@ repos: | |||
| args: [--line-width, "120", --profile, black] | |||
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| - repo: https://github.com/PyCQA/docformatter | |||
| rev: v1.7.5 | |||
| rev: eb1df34 | |||
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| @@ -0,0 +1,520 @@ | |||
| # anndata_similarity.py | |||
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Calculate the similarity of data sets and return the most similar data set in the atlas for the query data set
| @@ -268,6 +271,31 @@ def __init__( | |||
| inplace=inplace, **kwargs) | |||
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| @register_preprocessor("filter", "cell") | |||
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FilterCellsCommonMod: Filters single-cell data to retain only common cells between two modalities.
This transformation filters two single-cell modalities (mod1 and mod2) to retain only the cells
that are shared between them. Optionally, a solution dataset (sol) containing cell labels or annotations
can be filtered to match the common cells.
| @@ -169,6 +172,37 @@ def __call__(self, data: Data) -> Data: | |||
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| @register_preprocessor("normalize") | |||
| @add_mod_and_transform | |||
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Transform the data set using the tfidf method
| @@ -0,0 +1,112 @@ | |||
| { | |||
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Record the correspondence between atlas datasets and algorithms for statistical algorithm results
for more information, see https://pre-commit.ci
… celltype_annotation_automl
for more information, see https://pre-commit.ci
… celltype_annotation_automl
for more information, see https://pre-commit.ci
… celltype_annotation_automl
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| import functools | ||
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A decorator that modifies a class to add functionality for working with specific modalities (mod) in a mudata object.
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
… celltype_annotation_automl
for more information, see https://pre-commit.ci
… celltype_annotation_automl
for more information, see https://pre-commit.ci
… celltype_annotation_automl
for more information, see https://pre-commit.ci
for more information, see https://pre-commit.ci
… celltype_annotation_automl
for more information, see https://pre-commit.ci
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