spatialProximityScore

spatialProximityScore ¶

spatialProximityScore(
    data,
    label="spatial_pscore",
    plotScore="both",
    orderXAxis=None,
    color="grey",
    figsize=None,
    fileName="spatial_pscore.pdf",
    outputDir=None,
    saveDir=None,
    show=True,
    returnData=False,
    returnFig=False,
    dpi=300,
    transparent=False,
    sdataTable=None,
    **kwargs
)

Proximity volume and density scores, as a bar chart.

Reads the summary table that sp.tl.spatialProximityScore writes to uns[label] — one row per image, with a proximity volume (what fraction of all cells are in the interaction zone) and a proximity density (how enriched that zone is for the pair of interest).

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
`label`	`str`	Key in `uns` holding the proximity summary.	`'spatial_pscore'`
`plotScore`	`str`	`'both'`, or the name of a single score column to plot. Accepted for signature compatibility; the current implementation plots every column of the summary table.	`'both'`
`orderXAxis`	`list`	Explicit row order.	`None`
`color`	`str`	Bar colour.	`'grey'`
`figsize`	`tuple`	Figure size in inches. Scaled from the number of rows when `None`.	`None`
`fileName`	`str`	File name for the saved figure. The extension decides the format.	`'spatial_pscore.pdf'`
`outputDir`	`str`	Directory to save the figure in. When `None` nothing is written.	`None`
`saveDir`	`str`	Deprecated alias for `outputDir`, kept for scripts carried over from scimap. `outputDir` wins when both are given.	`None`
`show`	`bool`	Call `plt.show()` before returning. Set `False` in scripts and notebooks that save rather than display.	`True`
`returnData`	`bool`	Return the `DataFrame` behind the plot instead of drawing it.	`False`
`returnFig`	`bool`	Return `(fig, axes)`. With `returnData` as well, returns `(fig, axes, plotData)`.	`False`
`dpi`	`int`	Resolution of the saved figure.	`300`
`transparent`	`bool`	Save with a transparent background.	`False`
`sdataTable`	`str`	Which `SpatialData` table to read. Ignored for `AnnData` input, and optional when the store has exactly one table.	`None`

Returns:

Name	Type	Description
`result`	`None \| DataFrame \| tuple`	`None` by default; the summary table with `returnData=True`; `(fig, ax)` with `returnFig=True`.

Example

adata = sp.tl.spatialProximityScore(adata, proximity=["Treg", "ECAD+"])
sp.pl.spatialProximityScore(adata)