popv.algorithms.CELLTYPIST

popv.algorithms.CELLTYPIST#

class popv.algorithms.CELLTYPIST(batch_key='_batch_annotation', labels_key='_labels_annotation', result_key='popv_celltypist_prediction', method_kwargs=None, classifier_dict=None)[source]#

Class to compute Celltypist classifier.

Parameters:

  • batch_key (str | None (default: '_batch_annotation')) – Key in obs field of adata for batch information. Default is “_batch_annotation”.

  • labels_key (str | None (default: '_labels_annotation')) – Key in obs field of adata for cell-type information. Default is “_labels_annotation”.

  • result_key (str | None (default: 'popv_celltypist_prediction')) – Key in obs in which celltype annotation results are stored. Default is “popv_celltypist_prediction”.

  • method_kwargs (dict | None (default: None)) – Additional parameters for celltypist training. Options at celltypist.train().

  • classifier_dict (dict | None (default: None)) – Dictionary to supply non-default values for celltypist annotation. Options at celltypist.annotate().

Methods table#

compute_integration(adata)

Compute integration of adata inplace.

compute_umap(adata)

Compute UMAP embedding of adata inplace.

predict(adata)

Predict celltypes using Celltypist.

Methods#

abstractmethod CELLTYPIST.compute_integration(adata)[source]#

Compute integration of adata inplace.

abstractmethod CELLTYPIST.compute_umap(adata)[source]#

Compute UMAP embedding of adata inplace.

CELLTYPIST.predict(adata)[source]#

Predict celltypes using Celltypist.

Parameters:

adata – Anndata object. Results are stored in adata.obs[self.result_key].

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