AnnDatasetFromAnnData

class scvi.dataset.AnnDatasetFromAnnData(ad, batch_label='batch_indices', ctype_label='cell_types', class_label='labels', use_raw=False, cell_measurements_col_mappings=None)

Bases: scvi.dataset.dataset.GeneExpressionDataset

Forms a GeneExpressionDataset from a anndata.AnnData object.

Parameters

• ad (AnnDataAnnData) – anndata.AnnData instance.

• batch_label (strstr) – AnnData obs column name for batches

• ctype_label (strstr) – AnnData obs column name for cell_types

• class_label (strstr) – AnnData obs column name for labels

• use_raw (boolbool) – if True, copies data from .raw attribute of AnnData