stlearn.pl.plot_mask

stlearn.pl.plot_mask(adata: AnnData, library_id: Optional[str] = None, show_spot: bool = True, spot_alpha: float = 1.0, cmap: str = 'vega_20_scanpy', tissue_alpha: float = 1.0, mask_alpha: float = 0.5, spot_size: Union[float, int] = 6.5, show_legend: bool = True, name: str = 'mask_plot', dpi: int = 150, output: Optional[str] = None, show_axis: bool = False, show_plot: bool = True) → Optional[AnnData][source]

mask plot for sptial transcriptomics data.

Parameters:

  • adata – Annotated data matrix.

  • library_id – Library id stored in AnnData.

  • show_spot – Show spot or not

  • spot_alpha – Opacity of the spot.

  • cmap – Color map to use.

  • tissue_alpha – Opacity of the tissue.

  • mask_alpha – Opacity of the mask.

  • spot_size – Size of the spot.

  • show_axis – Show axis or not.

  • show_legend – Show legend or not.

  • name – Name of the output figure file.

  • dpi – DPI of the output figure.

  • output – Save the figure as file or not.

  • show_plot – Show plot or not

Return type:

Nothing