c2v.pl.group_connectivity

c2v.pl.group_connectivity(adata, basis='X_umap', color_bg=False, alpha_bg=0.5, s_bg=None, clip=(1, 2), ax=None, return_fig=False, uns_key='group_connectivity', title=None, show=True, linewidth=1.0, figsize=None)

Plot group connectivity on top of the embedding.

Parameters:

adata sc.AnnData

Annotated data matrix.

basis str

Key for embedding coordinates in adata.obsm.

color_bg bool

Whether to color the background points.

alpha_bg float

Alpha value for the background points.

s_bg float | None

Size of the background points.

clip tuple[float, float]

Clip values for the connectivity matrix.

ax matplotlib.axes.Axes | None

Axes object to plot on.

return_fig bool

Whether to return the figure object.

uns_key str

Key for group connectivity in adata.uns.

title str | None

Title for the plot.

show bool

Whether to show the plot.

linewidth float

Linewidth for the connections.

figsize tuple[float, float] | None

Figure size.

Return type:

Axes | Figure | None

Returns:

ax: matplotlib.axes.Axes | matplotlib.figure.Figure | None Axes object with the plot.