troutpy.tl.assess_diffusion

troutpy.tl.assess_diffusion#

troutpy.tl.assess_diffusion(sdata, gene_key='gene', distance_key='distance', copy=False)#

Computes goodness-of-fit metrics for the diffusion pattern of unassigned RNA by testing against a Rayleigh distribution. Also estimates the diffusion coefficient (D) based on the mean squared displacement (MSD).

Parameters:

  • sdata (spatialdata.SpatialData) – The spatial transcriptomics dataset.

  • gene_key (str) – The key for gene/transcript names in source_score.obs.

  • distance_key (str) – The key for RNA displacement distances.

  • copy (bool) – Whether to return a modified copy of sdata.

Returns:

If copy=True, returns a modified SpatialData object with results in sdata[‘xrna_metadata’]. Otherwise, modifies sdata in place.

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