alphapepttools.pp.nanlog

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alphapepttools.pp.nanlog#

alphapepttools.pp.nanlog(data, base=2, verbosity=1, layer=None, *, copy=False)#

Logarithmize a data matrix.

Apply arbitrary base logarithm transformation to AnnData.X, replacing invalid values with np.nan. Similar to the underlying numpy log functions, invalid values are replaced with np.nan, but a more detailed summary of which values were replaced is provided.

Current invalid values include: - NaN values - Zero values - Negative values - Positive infinity - Negative infinity

Parameters:

  • x (anndata.AnnData) – Input data; negatives and/or zeros are converted to np.nan

  • base (int) – Base of the logarithm. Defaults to 2 (log2).

  • verbosity (int, default 1) – If 1, log warnings for invalid values found in the data.

  • layer (Optional[str] (default: None)) – Name of the layer to transform. If None (default), the data matrix X is used.

  • copy (bool (default: False)) – Whether to return a modified copy (True) of the anndata object. If False (default) modifies the object inplace

Return type:

AnnData

Returns:

None | anndata.AnnData Log-transformed data with invalid values replaced by np.nan. If copy=False modifies the anndata object at layer inplace and returns None. If copy=True, returns a modified copy.

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