cytonormpy.CytoNorm.run_anndata_setup

cytonormpy.CytoNorm.run_anndata_setup#

CytoNorm.run_anndata_setup(adata, layer='compensated', reference_column='reference', reference_value='ref', batch_column='batch', sample_identifier_column='file_name', n_cells_reference=None, channels='markers', key_added='cyto_normalized', copy=False)#

Method to setup the data handling for anndata objects. Will instantiate a DataHandlerAnnData object.

Parameters:

  • adata (AnnData) – The AnnData object

  • layer (str) – The layer in adata.uns containing the compensated expression values

  • reference_column (str) – The column in adata.obs that specifies whether a sample is used for reference and is therefore present in all batches.

  • reference_value (str) – Specifies the value that is considered a reference. Defaults to ‘ref’

  • batch_column (str) – The column in adata.obs that specifies the batch.

  • sample_identifier_column (str) – Specifies the column in adata.obs that is unique to the samples.

  • n_cells_reference (Optional[int]) – If there are no reference samples for a batch, this number will define how many cells from a batch are subsampled to comprise the new reference file.

  • channels (Union[list[str], str, Literal['all', 'markers']]) – Can be a list of detectors (e.g. BV421-A), a single channel or ‘all’ or ‘markers’. If markers, channels containing ‘FSC’, ‘SSC’, ‘Time’, ‘AF’ and CyTOF technicals will be excluded.

  • key_added (str) – The name of the layer in adata.layers where the normalized data are inserted to.

Return type:

None, appends ._datahandler attribute.

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