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Docs #54

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merged 2 commits into from
Apr 27, 2024
Merged

Docs #54

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003dded
fix doc strings
Apr 27, 2024
4b85d80
fix docs
Apr 27, 2024
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16 changes: 10 additions & 6 deletions scenvi/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,10 @@ def __call__(self, x, mode="spatial", key=random.key(0)):

@struct.dataclass
class Metrics(metrics.Collection):
"""
:meta private:
"""

enc_loss: metrics.Average
dec_loss: metrics.Average
enc_corr: metrics.Average
Expand Down Expand Up @@ -257,12 +261,12 @@ def compute_covet(
"""
Compute niche covariance matrices for spatial data, run with scenvi.compute_covet

:param spatial_data (anndata): anndata with spatial data, with an obsm indicating spatial location of spot/segmented cell
:param k (int): number of nearest neighbours to define niche (default 8)
:param g (int): number of HVG to compute COVET representation on (default 64)
:param genes (list of str): list of genes to keep for niche covariance (default []
:param spatial_key (str): obsm key name with physical location of spots/cells (default 'spatial')
:param batch_key (str): obs key name of batch/sample of spatial data (default 'batch' if in spatial_data.obs, else -1)
:param spatial_data: (anndata) spatial data, with an obsm indicating spatial location of spot/segmented cell
:param k: (int) number of nearest neighbours to define niche (default 8)
:param g: (int) number of HVG to compute COVET representation on (default 64)
:param genes: (list of str) list of genes to keep for niche covariance (default []
:param spatial_key: (str) obsm key name with physical location of spots/cells (default 'spatial')
:param batch_key: (str) obs key name of batch/sample of spatial data (default 'batch' if in spatial_data.obs, else -1)

:return COVET: niche covariance matrices
:return COVET_SQRT: matrix square-root of niche covariance matrices for approximate OT
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