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scirpy.io.from_dandelion

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scirpy.io.from_dandelion#

scirpy.io.from_dandelion(dandelion, transfer=False, to_mudata=False, **kwargs)#

Import data from Dandelion ([SRB+21]).

Internally calls dandelion.to_scirpy.

Note

Since scirpy v0.13, there are no restrictions on the AIRR data that can be stored in the scirpy data structure, except that each receptor chain needs to be associated with a cell.

The scirpy Immune receptor (IR) model is now applied in later step using the index_chains() function.

For more information, see Storing AIRR rearrangement data in AnnData.

Parameters:

  • dandelion – a dandelion.Dandelion instance

  • transfer (bool (default: False)) – Whether to execute dandelion.tl.transfer to transfer all data to the anndata.AnnData instance.

  • to_mudata (bool (default: False)) – Return MuData object instead of AnnData object.

  • **kwargs – Additional arguments passed to dandelion.to_scirpy.

Return type:

AnnData

Returns:

AnnData object with AIRR data in obsm["airr"] for each cell. For more details see Storing AIRR rearrangement data in AnnData.

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