spatialvi.utils.plot_spatial

Contents

spatialvi.utils.plot_spatial#

spatialvi.utils.plot_spatial(adata, color=None, spatial_key='spatial', size=1.0, alpha=1.0, cmap='viridis', ax=None, show=True, **kwargs)[source]#

Plot cells in spatial coordinates.

Parameters:

  • adata (AnnData) – AnnData object.

  • color (str | list[str] | None) – Key in obs or var_names to color by.

  • spatial_key (str) – Key in obsm for spatial coordinates.

  • size (float) – Point size.

  • alpha (float) – Point transparency.

  • cmap (str) – Colormap for continuous values.

  • ax (Axes | None) – Matplotlib axes to use.

  • show (bool) – Whether to show the plot.

  • **kwargs – Additional arguments for scatter.

  • adata (AnnData)

  • color (str | list[str] | None)

  • spatial_key (str)

  • size (float)

  • alpha (float)

  • cmap (str)

  • ax (Axes | None)

  • show (bool)

Return type:

Axes | None

Returns:

Matplotlib axes if show=False.

Contents