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

Analyze Visium fluorescence data