cospar.pp.get_X_clone

cospar.pp.get_X_clone(adata, clone_data_cell_id, clone_data_barcode_id, reference_cell_id=None, reference_clone_id=None)

Build the X_clone matrix from data.

Convert the raw clonal data table (long format): [clone_data_cell_id,clone_data_barcode_id] to X_clone (wide format) based on the unique cell id ordering in adata

Parameters

adata : AnnData object

We assume that adata.obs_names have been initialized.

clone_data_cell_id : list

The list of cell id for each corresponding sequenced barcode.

clone_data_barcode_id : list

The list of barcode id from sequencing. It has the same shape as clone_data_cell_id.

reference_cell_id : list, optional (default: None)

A list of uniuqe cell id. X_clone will be generated based on its cell id ordering. This has to be provided to match the cell ordering in the adata object.

reference_clone_id : list, optional (default: None)

A list of uniuqe clone id. If provided, X_clone will be generated based on its barcode ordering.

Returns

Update adata.obsm[‘X_clone’] (sp.spmatrix)