SpatialQuery.interactive_motif

SpatialQuery.spatial_query.interactive_motif(sp, zarr_path, spatialSpotRadius=1, use_adata_store=False)[source]

Create an interactive Vitessce widget to explore spatial motifs.

Builds a minimal AnnData containing cell type labels, spatial coordinates, and (optionally) gene expression from the SpatialQuery object, writes it to a Zarr store, and launches a Vitessce widget with the SpatialQueryPlugin. The widget provides interactive panels for spatial visualization, cell type selection, motif enrichment analysis, and gene expression exploration.

Parameters:

  • sp (spatial_query) – An initialized SpatialQuery instance. If build_gene_index=False and sp.adata is not None, gene expression data will be included in the widget for feature-level exploration.

  • zarr_path (str) – Path where the Zarr store will be written. If the path already exists, its contents will be overwritten with a warning.

  • spatialSpotRadius (float, default=1) – Radius for spatial spots in the Vitessce visualization. Adjust based on data density and spatial coordinate scale.

  • use_adata_store (bool, default=False) – If True, pass the zarr path via adata_store (for HubMAP workspace). If False, pass via adata_path (for local usage).

Returns:

A Vitessce widget that can be displayed in a Jupyter notebook. The widget contains the following views:

  • Spatial view: scatter plot of cells colored by cell type

  • Layer controller: toggle visibility and appearance of layers

  • Cell sets: browse and select cell types

  • SpatialQuery: interactive motif enrichment query panel

  • SpatialQuery Heatmap: heatmap of motif enrichment results

  • Feature list: gene selection panel (only when expression data is available)

Return type:

ipywidgets.Widget

Notes

This function requires the vitessce Python package (with the SpatialQueryPlugin) to be installed. Install it via:

pip install vitessce[all]

The generated widget is designed for use in Jupyter notebooks (JupyterLab or Jupyter Notebook).

Examples

>>> from SpatialQuery.spatial_query import spatial_query, interactive_motif
>>> sq = spatial_query(adata, spatial_key='X_spatial', label_key='cell_type')
>>> widget = interactive_motif(sq, zarr_path='./my_data.zarr')
>>> widget