thor.pl.spot_over

thor.pl.spot_over(ad, ad_spot, spot_scale=1, figsize=None, spot_cmap='viridis', spot_color_obs_key=None, spot_facecolor=None, spot_alpha=0.5, spot_linewidth=0.5, **sc_kwargs)[source]

Plot spatial expression data with spots on top.

Parameters:

  • ad (anndata.AnnData) – Annotated data matrix at the cell level.

  • ad_spot (anndata.AnnData) – Annotated data matrix at the spot level.

  • spot_scale (float, optional (default: 1)) – Scale factor for spot size.

  • figsize (tuple, optional (default: None)) – Figure size in full resolution.

  • spot_cmap (str, optional (default: ‘viridis’)) – Colormap for spot colors.

  • spot_color_obs_key (str, optional (default: None)) – Key for observation in ad_spot that contains spot colors.

  • spot_facecolor (str, optional (default: None)) – Face color for spots.

  • spot_alpha (float, optional (default: 0.5)) – Alpha value for spots.

  • spot_linewidth (float, optional (default: 0.5)) – Line width for spots.

  • **sc_kwargs (keyword arguments) – Keyword arguments for spatial().

Return type:

Depending on scanpy settings returns axes or list of axes.