squidpy.pl.extract

squidpy.pl.extract(adata, obsm_key='img_features', prefix=None)

Create a temporary anndata.AnnData object for plotting.

Move columns from anndata.AnnData.obsm ['{obsm_key}'] to anndata.AnnData.obs to enable the use of scanpy.plotting functions.

Parameters:

• adata (AnnData) – Annotated data object.

• obsm_key (Union[List[str], str]) – Entries in anndata.AnnData.obsm that should be moved to anndata.AnnData.obs.

• prefix (Union[List[str], str, None]) – Prefix to prepend to each column name. Should be a :class;`list` if obsm_key is a list. If None, use the original column names.

Return type:

AnnData

Returns:

: Temporary anndata.AnnData object with desired entries in anndata.AnnData.obs.

Raises:

ValueError – If number of prefixes does not fit to number of obsm_keys.

Notes

If anndata.AnnData.obs ['{column}'] already exists, it will be overwritten and a warning will be issued.

Gallery

Extract texture features

Extract histogram features

Extract summary features

Extract custom features

Extract segmentation features

Extract image features

Plot features in adata.obsm