mantispy.get.to_dataframe

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mantispy.get.to_dataframe#

mantispy.get.to_dataframe(adata, layer=None, metadata=True, features=None)#

Wide, pycytominer-shaped frame: Metadata_ columns first, then features.

Use it to pass profiles to pycytominer, cytominer-eval and other tools that expect a flat table.

Parameters:

  • adata (AnnData) – Object to read.

  • layer (str | None (default: None)) – Layer to read instead of X.

  • metadata (bool (default: True)) – Put the Metadata_ columns of obs in front of the feature columns.

  • features (Sequence[str] | None (default: None)) – Features to take, in the order given, defaulting to every feature in var order.

Return type:

DataFrame

Returns:

A frame indexed by obs_names, with one column per feature and, unless metadata is off, the Metadata_ columns of obs before them.

Raises:

KeyError – A name in features is not in var_names.

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