sparrow.sh.filter_shapes_layer

sparrow.sh.filter_shapes_layer(sdata, table_layer, labels_layer, prefix_filtered_shapes_layer, shapes_layers_to_filter=None)

Filter shapes in a SpatialData object.

Cells that do not appear in table_layer (with _REGION_KEY equal to labels_layer) will be removed from the shapes layers, via the _INSTANCE_KEY of sdata.tables[table_layer].obs) and the index of the shapes layers in the sdata object. Only shapes layers of sdata in same coordinate system as the labels_layer will be considered. Polygons that are filtered out from a shapes layer (e.g. with name “shapes_example”) will be added as a new shapes layer with name prefix_filtered_shapes_layer + “_” + “shapes_example”.

Parameters:

• sdata (SpatialData) – The SpatialData object,

• table_layer (str) – The name of the table layer.

• labels_layer (str) – The name of the labels layer.

• prefix_filtered_shapes_layer (str) – The prefix for the name of the new shapes layer consisting of the polygons that where filtered out from a shapes layer.

• shapes_layers_to_filter (list[str] | None (default: None)) – List of names of the shapes layers to filter. If None, all shapes layers in sdata that match the coordinate system of the labels layer will be filtered.

Return type:

SpatialData

Returns:

: The updated sdata object.