spateo.plotting.interactive¶

Submodules¶

spateo.plotting.interactive.agg

Functions¶

`cellbin_select`(...)	Select cells by drawing a polygon on a binning image of the spatial transcriptomics data.
`contours`(→ plotly.graph_objects.Figure)	Interactively display UMI density bins.
`select_polygon`(→ matplotlib.widgets.PolygonSelector)	Display raw data within an AnnData with interactive polygon selection.

Package Contents¶

spateo.plotting.interactive.cellbin_select(adata: anndata.AnnData, binsize: int = 50, spatial_key: str = 'spatial', layer: str | None = None, scale: float = 0.5, scale_unit: str = 'um', return_all: bool = False) → matplotlib.widgets.PolygonSelector | Tuple[matplotlib.widgets.PolygonSelector, anndata.AnnData][source]¶

Select cells by drawing a polygon on a binning image of the spatial transcriptomics data.

Parameters:

adata: Anndata containing segmented cells.
binsize: Size of bins to use for aggregating the expression data.
spatial_key: The key to the spatial coordinates in the adata.obsm attribute.
layer: The layer to use for the expression data. Defaults to None (adata.X will be used).
scale: The scale of the spatial coordinates.
scale_unit: The unit of the spatial coordinates.
return_all: Whether to return both the PolygonSelector and the aggregated image.

Returns:

When return_all is False, only a PolygonSelector object will be returned; otherwise both a tuple of both: the aggregated image data and the PolygonSelector object will be used.

spateo.plotting.interactive.contours(adata: anndata.AnnData, layer: str, colors: List | None = None, scale: float = 0.05) → plotly.graph_objects.Figure[source]¶

Interactively display UMI density bins.

Parameters:

adata: Anndata containing aggregated UMI counts.
layer: Layer to display
colors: List of colors.
scale: Scale width and height by this amount.

Returns:

A Plotly figure

spateo.plotting.interactive.select_polygon(adata: anndata.AnnData, layer: str, out_layer: str | None = None, ax: matplotlib.axes.Axes | None = None, background: str | None = None, **kwargs) → matplotlib.widgets.PolygonSelector[source]¶

Display raw data within an AnnData with interactive polygon selection.

Parameters:

adata: Anndata containing aggregated UMI counts.
layer: Layer to display. Defaults to X.
out_layer: Layer to output selection result as a boolean mask. Defaults to {layer}_selection.
ax: Axes to plot.
background: string or None (optional, default ‘None`) The color of the background. Usually this will be either ‘white’ or ‘black’, but any color name will work. Ideally one wants to match this appropriately to the colors being used for points etc. This is one of the things that themes handle for you. Note that if theme is passed then this value will be overridden by the corresponding option of the theme.
**kwargs: Additional keyword arguments are all passed to spateo.pl.imshow().