Nbhd color values

[cornhundred]

PR #291: Neighborhood Attribute Coloring & Enrichment Linking Improvements

Summary

This PR adds support for coloring neighborhoods by numerical attributes (gene expression, GDF properties) and improves the Clustergram-Enrich widget linking using jslink for more reliable communication.

New Features

🎨 Neighborhood Attribute Coloring

• New nbhd_adata parameter on Landscape: Pass an AnnData with neighborhoods as obs and attributes (genes, populations, etc.) as var

  landscape = dega.viz.Landscape(
      technology='Xenium',
      base_url=base_url,
      adata=adata,
      nbhd_adata=adata_nbg,  # NEW: neighborhood × gene matrix
  )

• Dropdown for GDF attributes: Numeric columns from neighborhood GeoDataFrame are now available in a color dropdown (e.g., area, perimeter)

• nbhd_gene entity type: New entity type for Clustergrams where rows are genes aggregated at the neighborhood level

  mat_nbg = dega.clust.Matrix(
      adata_nbg, 
      col_entity='nbhd',
      row_entity='nbhd_gene'  # Enables enrichment analysis
  )

• data_type field in AxisEntity: Allows specifying the underlying data type for analysis purposes, independent of the spatial entity

🔗 Simplified Clustergram-Enrich Linking

• Replaced Python observers with jslink: More reliable trait synchronization that works even when Python kernel restarts

  jslink((cgm, "selected_genes"), (enrich, "gene_list"))

• Removed link_clustergram_to_enrich function: No longer needed since jslink handles the connection

• Simplified API: Removed row_enrich/col_enrich parameters (jslink syncs all selected genes)

Bug Fixes

• Neighborhoods with zero expression now transparent: Fixed the minimum opacity issue that made zero-valued neighborhoods appear pink

Files Changed

File	Changes
src/celldega/viz/widget.py	Added nbhd_adata parameter, attribute request/response traitlets
src/celldega/viz/__init__.py	Simplified enrichment linking with jslink
src/celldega/clust/constants.py	Added data_type field and nbhd_gene entity
js/ui/nbhd_attr_dropdown.js	New dropdown UI for neighborhood coloring
js/deck-gl/layers/nbhd_layer.js	Support for gene expression coloring
js/widget_interactions/update_ist_landscape_from_cgm.js	Handle nbhd_gene and nbhd_var entities

Usage Example

# Create neighborhood gene expression matrix
adata_nbg = dega.tl.calc_nbhd_by_gene(adata, adata_nbhd)

# Create Landscape with neighborhood data
landscape = dega.viz.Landscape(
    technology='Xenium',
    base_url=base_url,
    adata=adata,
    nbhd_adata=adata_nbg,
)

# Create Clustergram with nbhd_gene entity
mat_nbg = dega.clust.Matrix(adata_nbg, col_entity='nbhd', row_entity='nbhd_gene')
mat_nbg.norm(axis='row', by='zscore')
mat_nbg.cluster()
cgm_nbg = dega.viz.Clustergram(matrix=mat_nbg)

# Display with enrichment
dega.viz.landscape_clustergram(landscape, cgm_nbg, enrich=True)