neighExp

neighExp

neighExp(
    data,
    xCoordinate="X_centroid",
    yCoordinate="Y_centroid",
    zCoordinate=None,
    method="radius",
    radius=30,
    knn=10,
    imageId="imageid",
    layer="raw",
    log=True,
    subset=None,
    label="neighExp",
    verbose=True,
    outputDir=None,
    streamData=False,
    sdataTable=None,
)

Neighbourhood-weighted expression (spatial lag) for every cell.

For each cell, average the expression of its neighbours, producing a cell x marker matrix in which each value describes the cell's surroundings. Clustering it with cluster(mode="spatial") gives Recurrent Cellular Neighbourhoods defined by expression rather than by cell type.

The neighbour weights are assembled directly as row/column/value arrays and multiplied through a sparse matrix, so the lag is one csr_matrix product rather than a loop over cells.

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
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'
layer	str	Which matrix to average. 'raw' uses .raw.X, None uses .X, any other string names a key in .layers.	'raw'
log	bool	Apply log1p before averaging.	True
subset	str	Process only this image.	None
label	str	Key in uns the lagged matrix is written to.	'neighExp'
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 the cell x marker lagged matrix in uns[label]. None in streaming mode.

Example

adata = sp.tl.neighExp(adata, method="radius", radius=30, layer="raw")

# Cluster the environment rather than the cell.
adata = sp.tl.cluster(
    adata, mode="spatial", layer="neighExp", method="kmeans", k=8,
    label="expressionNeighbourhood",
)
sp.pl.spatialScatterPlot(adata, colorBy="expressionNeighbourhood", s=3)