squidpy.pl.Interactive

class squidpy.pl.Interactive(img, adata, **kwargs)[source]

Interactive viewer for spatial data.

Parameters:

  • img (ImageContainer) – High-resolution image.

  • adata (AnnData) – Annotated data object.

  • spatial_key – Key in anndata.AnnData.obsm where spatial coordinates are stored.

  • library_key – Key in adata.AnnData.obs specifying mapping between observations and library ids. Required if the container has more than 1 Z-dimension.

  • library_id – Subset of library ids to visualize. If None, visualize all library ids.

  • cmap – Colormap for continuous variables.

  • palette – Colormap for categorical variables in anndata.AnnData.obs. If None, use scanpy’s default.

  • blending – Method which determines how RGB and alpha values of napari.layers.Shapes are mixed.

  • symbol –

    Symbol to use for the spots. Valid options are:

    • ’disc’ - circle.

    • ’square’ - square.

Methods

close()

Close the viewer.

screenshot([return_result, dpi, save, ...])

Plot a screenshot of the viewer's canvas.

show([restore])

Launch the napari.Viewer.

Attributes

adata

Annotated data object.