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, usescanpy
’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.
Attributes
Annotated data object.
Methods
close
()Close the viewer.
screenshot
([return_result, dpi, save, ...])Plot a screenshot of the viewer's canvas.
show
([restore])Launch the
napari.Viewer
.