omicverse.space.STT

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omicverse.space.STT#

class omicverse.space.STT(adata, spatial_loc='xy_loc', region='Region')[source]#

Spatial Transition Tensor (STT) analysis class.

STT models spatial dynamics and transitions by learning spatial-temporal patterns in spatial transcriptomics data using transition tensors. This class provides methods for analyzing cell state transitions, developmental trajectories, and spatial dynamics in tissue organization.

Parameters:

  • adata (AnnData) – Spatial AnnData containing spliced/unspliced layers and coordinates.

  • spatial_loc (str, default='xy_loc') – Coordinate key in adata.obsm.

  • region (str, default='Region') – Region annotation column in adata.obs.

  • Attributes –

    adata: AnnData

    Input annotated data matrix.

    adata_aggr: AnnData or None

    Aggregated data after training.

    spatial_loc: str

    Key for spatial coordinates.

    region: str

    Key for region annotations.

  • Examples – 

    >>> import scanpy as sc
>>> import omicverse as ov
>>> # Load data with spliced/unspliced counts
>>> adata = sc.read_h5ad('spatial_velocity.h5ad')
>>> # Initialize STT object
>>> stt = ov.space.STT(
...     adata,
...     spatial_loc='spatial',
...     region='tissue_region'
... )
>>> # Estimate cell stages
>>> stt.stage_estimate()
>>> # Train the model
>>> stt.train(n_states=10)

__init__(adata, spatial_loc='xy_loc', region='Region')[source]#

Initialize STT spatial transition analysis object.

Parameters:

  • adata (AnnData) – Input AnnData with spatial and velocity-related layers.

  • spatial_loc (str, default='xy_loc') – Coordinate key in adata.obsm.

  • region (str, default='Region') – Region key in adata.obs.

Methods

__init__(adata[, spatial_loc, region])

Initialize STT spatial transition analysis object.

compute_pathway(pathway_dict[, n_components])

Compute spatial pathways for cell transitions.

construct_landscape([coord_key])

Construct spatial landscape for transition analysis.

infer_lineage(**kwargs)

Infer cell lineage relationships from spatial transitions.

load(adata, adata_aggr)

Load pre-trained STT model data.

plot_landscape(**kwargs)

Plot spatial landscape visualization.

plot_pathway([label_fontsize])

Plot spatial transition pathways.

plot_sankey(vector1, vector2)

Plot Sankey diagram for cell transitions.

plot_tensor(list_attractor, **kwargs)

Plot spatial transition tensors.

plot_tensor_pathway(pathway_name, **kwargs)

Plot tensor-based spatial pathways.

plot_top_genes(**kwargs)

Plot top genes driving spatial transitions.

stage_estimate()

Estimate cell stages using joint clustering of spliced and unspliced data.

train([n_states, n_iter, ...])

Train the STT spatial transition model.
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