troutpy.tl.spatial_colocalization

troutpy.tl.spatial_colocalization#

troutpy.tl.spatial_colocalization(sdata, coord_keys=None, gene_key='gene', resolution=1000, square_size=20, n_threads=1, threshold_colocalized=1, copy=False)#

Compute the proportion of spatially colocalized extracellular transcripts per gene.

Uses kernel density estimation (LazyKDE) to bin transcripts into a spatial grid, then calculates for each gene the fraction of bins whose count exceeds threshold_colocalized. Results are stored in sdata["xrna_metadata"].var["proportion_of_colocalized"].

Parameters:

  • sdata (spatialdata.SpatialData) – SpatialData object with a "transcripts" points layer containing "extracellular" and gene_key columns, and an "xrna_metadata" table (created automatically if absent).

  • coord_keys (list of str, optional) – Spatial coordinate column names. Defaults to ["x", "y"].

  • gene_key (str, optional) – Column in the transcript layer with gene identifiers. Defaults to "gene".

  • resolution (int, optional) – Grid resolution passed to LazyKDE. Defaults to 1000.

  • square_size (int, optional) – Bin size (in coordinate units) for the KDE grid. Defaults to 20.

  • n_threads (int, optional) – Number of threads for LazyKDE processing. Defaults to 1.

  • threshold_colocalized (int, optional) – Minimum per-bin count for a bin to be considered colocalized. Defaults to 1.

  • copy (bool, optional) – If True, return the updated SpatialData object; otherwise modify in place and return None. Defaults to False.

Returns:

spatialdata.SpatialData or None Updated SpatialData with "proportion_of_colocalized" added to sdata["xrna_metadata"].var if copy=True; otherwise None.

Contents