spatialInteractionNetwork

spatialInteractionNetwork ¶

spatialInteractionNetwork(
    data,
    spatialCooccurrence="spatialCooccurrence",
    pVal=0.05,
    cmap="vlag",
    nodeColor="#22333b",
    nodeSize=None,
    alpha=0.9,
    figsize=None,
    fontSize=12,
    fontColor="white",
    subsetPhenotype=None,
    fileName="spatialInteractionNetwork.pdf",
    outputDir=None,
    saveDir=None,
    show=True,
    returnData=False,
    returnFig=False,
    dpi=300,
    transparent=False,
    sdataTable=None,
)

Significant cell-type interactions as a circular node-edge network.

Cell types are laid out evenly on a circle and an edge is drawn for every pair whose co-occurrence p-value is below pVal. It answers "which cell types interact at all" faster than reading a heatmap.

Reads the same uns key as sp.pl.spatialCooccurrence, averaging across images.

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
`spatialCooccurrence`	`str`	Key in `uns` holding the result. Falls back to `'spatial_interaction'`.	`'spatialCooccurrence'`
`pVal`	`float`	An edge is drawn when the pair's p-value is below this.	`0.05`
`cmap`	`str`	Accepted for signature compatibility with scimap; edges are drawn black.	`'vlag'`
`nodeColor`	`str`	Node fill colour.	`'#22333b'`
`nodeSize`	`float`	Node marker area. Defaults to 600.	`None`
`alpha`	`float`	Edge opacity.	`0.9`
`figsize`	`tuple`	Figure size in inches. Defaults to `(6, 6)`.	`None`
`fontSize`	`int`	Node label font size.	`12`
`fontColor`	`str`	Node label colour.	`'white'`
`subsetPhenotype`	`str \| list`	Keep only these phenotypes as nodes.	`None`
`fileName`	`str`	File name for the saved figure. The extension decides the format.	`'spatialInteractionNetwork.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 p-value matrix behind the edges with `returnData=True`; `(fig, ax)` with `returnFig=True`.

Example

adata = sp.tl.spatialCooccurrence(adata, phenotype="phenotype", permutation=1000)
sp.pl.spatialInteractionNetwork(adata, pVal=0.01)