add_cell_labeling

besca.Import.add_cell_labeling(adata, filepath, label='celltype')[source]

add a labeling written out in the FAIR formating to adata.obs

A laveling contained in the FAIR compliant cell2labels.tsv is added to adata.obs. The string supplied in the parameter label is used to name the column in adata.obs that contains the imported labeling.

All cells that are not labeled in the cell2labels.tsv will be annotated with ‘not labeled’.

Parameters:

  • adata (AnnData) – the AnnData object whose obs should be updated

  • filepath (str) – filepath to the cell2labels.tsv that is to be appended to adata.obs

  • label (str | default = ‘celltype’) – string indicating the label that is to be added to the annotation that is being imported

Returns:

updates the supplied AnnData object

Return type:

None