omicverse.single.MetaTiME

omicverse.single.MetaTiME#

class omicverse.single.MetaTiME(adata, mode='table')[source]#

MetaTiME wrapper for tumor microenvironment cell-state annotation.

Parameters:

  • adata (anndata.AnnData) – AnnData to annotate with MetaTiME meta-components.

  • mode (str, optional, default='table') – Output mapping mode for component-to-cell-state interpretation.

Returns:

Initializes MetaTiME resources and annotation mode.

Return type:

None

Examples

>>> TiME_object = ov.single.MetaTiME(adata, mode="table")
__init__(adata, mode='table')[source]#

Initialize MetaTiME model resources and annotation table.

Parameters:

  • adata (anndata.AnnData) – AnnData object for MetaTiME annotation.

  • mode (str) – Name-mapping mode in metatime.mecs.load_mecname. Choose from 'mecnamedict', 'table' or 'meciddict'.

Methods

__init__(adata[, mode])

Initialize MetaTiME model resources and annotation table.

overcluster([resolution, random_state, ...])

Perform high-resolution Leiden clustering for MetaTiME input.

plot([basis, cluster_key, fontsize, ...])

Plot MetaTiME annotations with optional label collision adjustment.

predictTiME([save_obs_name])

Predict tumor microenvironment cell states for each cell.
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