spatialAggregate

spatialAggregate

spatialAggregate(
    data,
    xCoordinate="X_centroid",
    yCoordinate="Y_centroid",
    zCoordinate=None,
    purity=60,
    phenotype="phenotype",
    method="radius",
    radius=30,
    knn=10,
    imageId="imageid",
    subset=None,
    verbose=True,
    label="spatialAggregate",
    outputDir=None,
    maxWorkers=None,
    streamData=False,
    sdataTable=None,
)

Find local aggregates of a single cell type.

For every cell, look at its neighbourhood and take the most common phenotype there. When that phenotype accounts for at least purity percent of the neighbourhood, the cell is labelled with it; otherwise it is labelled 'non-significant'. The result is a map of where each cell type forms coherent patches rather than scattered individuals.

purity is the knob that matters: at 60 you get generous, contiguous regions; at 90 only dense cores survive.

Parameters:

Name	Type	Description	Default
data	(AnnData | SpatialData | str, required)	The cell table. An AnnData, a path to an .h5ad file, a SpatialData object, or a path to a .zarr SpatialData store.	required
xCoordinate	str	Column in obs holding x positions.	'X_centroid'
yCoordinate	str	Column in obs holding y positions.	'Y_centroid'
zCoordinate	str	Column in obs holding z positions. Leave as None for 2D data; set it and the neighbourhood search becomes three-dimensional.	None
purity	int	Minimum percentage of the neighbourhood that the dominant phenotype must occupy for a cell to be labelled. Between 1 and 100.	60
phenotype	str	Column in obs holding the cell type labels.	'phenotype'
method	str	How neighbourhoods are defined. 'radius' takes every cell within radius pixels; 'knn' takes the knn nearest cells regardless of distance.	'radius'
radius	float	Neighbourhood radius in the units of the coordinate columns, normally pixels. Used when method='radius'.	30
knn	int	Number of nearest neighbours. Used when method='knn'.	10
imageId	str	Column in obs holding image identifiers. Neighbourhoods never cross images.	'imageid'
subset	str	Process only this image.	None
label	str	Column in obs the aggregate labels are written to.	'spatialAggregate'
maxWorkers	int	Cap on parallel workers. Defaults to max(1, cpu_count() - 1). Lower it to cut peak memory.	None
verbose	bool	Print progress messages.	True
outputDir	str	Directory to write the updated object to. With None the object is returned instead.	None
streamData	bool	Run out of core against an .h5ad path with CAP-AnnData, reading only the sections this function needs and writing back only what it changes. Requires data to be a path; the file is updated in place and None is returned.	False
sdataTable	str	Which SpatialData table to work on. Ignored for AnnData input, and optional when the store has exactly one table.	None

Returns:

Name	Type	Description
adata	AnnData | SpatialData | None	The updated object with obs[label] naming the dominant phenotype, or 'non-significant'. None in streaming mode.

Example

adata = sp.tl.spatialAggregate(
    adata, phenotype="phenotype", method="radius", radius=30, purity=60
)
sp.pl.spatialScatterPlot(adata, colorBy="spatialAggregate", s=3)

# Only dense cores.
adata = sp.tl.spatialAggregate(adata, purity=90, label="dense_aggregates")