liana.pl.connectivity

liana.pl.connectivity(adata, idx, spatial_key='spatial', connectivity_key='spatial_connectivities', size=1, figure_size=(5.4, 5), return_fig=True)

Plot spatial connectivity weights.

Parameters:

adata AnnData

Annotated data object.

idx int

Column index of the connectivity weights to plot.

spatial_key str (default: 'spatial')

Key in adata.obsm that contains the spatial coordinates.

connectivity_key str (default: 'spatial_connectivities')

Key in adata.obsp that contains the spatial connectivity matrix. Default is 'spatial_connectivities'.

size float (default: 1)

Size of the points

figure_size tuple[float, float] (default: (5.4, 5))

Figure x,y size

return_fig bool (default: True)

bool whether to return the fig object.

Return type:

plotnine.ggplot | None

Returns:

The resulting connectivity plot.

Raises:

AssertionError – If connectivity_key or spatial_key are not in adata.obsp or adata.obsm respectively.

Examples

idx picks one spot, and the plot shows how strongly every other spot is connected to it under the kernel of liana.pp.spatial_neighbors():

>>> import liana as li
>>> adata = li.ds.generate_toy_spatial()
>>> p = li.pl.connectivity(adata, idx=0)