32 lines
1.1 KiB
Python
32 lines
1.1 KiB
Python
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def subset_vars(adata, subset_col):
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"""Subset AnnData object on highly variable genes
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Parameters
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----------
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adata : AnnData
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Annotated data object
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subset_col : str
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Name of the boolean column in `adata.var` that contains the information if features should be used or not
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Returns
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-------
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AnnData
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Copy of `adata` with subsetted features
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"""
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if subset_col not in adata.var.columns:
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raise ValueError(
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f"Requested to use .var column '{subset_col}' as a selection of genes, but the column is not available."
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)
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if adata.var[subset_col].dtype == "boolean":
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assert adata.var[subset_col].isna().sum() == 0, (
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f"The .var column `{subset_col}` contains NaN values. Can not subset data."
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)
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adata.var[subset_col] = adata.var[subset_col].astype("bool")
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assert adata.var[subset_col].dtype == "bool", (
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f"Expected dtype of .var column '{subset_col}' to be `bool`, but found {adata.var[subset_col].dtype}. Can not subset data."
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)
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return adata[:, adata.var[subset_col]].copy()
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