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Add render_graph for spatial connectivity visualization#592

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timtreis merged 1 commit into
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feature/render-graph
May 11, 2026
Merged

Add render_graph for spatial connectivity visualization#592
timtreis merged 1 commit into
mainfrom
feature/render-graph

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@timtreis timtreis commented Apr 16, 2026 •
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Summary

  • Adds sdata.pl.render_graph() to render spatial graph edges from adjacency matrices stored in table.obsp, using element centroids for coordinates via spatialdata.get_centroids()
  • Supports shapes, points, and labels elements
  • Includes groups + group_key filtering (both-endpoints semantics) and auto-discovery of element/table when unambiguous

API

# Basic: edges over shapes
sdata.pl.render_graph("cells", connectivity_key="spatial").pl.render_shapes("cells").pl.show()

# Full composition: image + graph + labels
sdata.pl.render_images("he").pl.render_graph("seg", table_name="table").pl.render_labels("seg").pl.show()

# Filtered: only tumor-to-tumor edges
sdata.pl.render_graph("cells", group_key="cell_type", groups=["tumor"]).pl.render_shapes("cells", color="cell_type").pl.show()

Implementation details

  • connectivity_key accepts full obsp key or prefix (auto-resolves "spatial" → "spatial_connectivities")
  • No networkx dependency — direct sparse matrix upper triangle → LineCollection
  • Rasterized by default for performance

@timtreis timtreis mentioned this pull request Apr 16, 2026
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codecov-commenter commented Apr 16, 2026 •
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Codecov Report

❌ Patch coverage is 80.25890% with 61 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.47%. Comparing base (84e5da7) to head (35ee4ce).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_plot/pl/utils.py 70.50% 22 Missing and 19 partials ⚠️
src/spatialdata_plot/pl/render.py 86.46% 7 Missing and 11 partials ⚠️
src/spatialdata_plot/pl/basic.py 85.71% 0 Missing and 2 partials ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #592      +/-   ##
==========================================
+ Coverage   77.07%   77.47%   +0.39%     
==========================================
  Files          11       11              
  Lines        3280     3569     +289     
  Branches      774      837      +63     
==========================================
+ Hits         2528     2765     +237     
- Misses        454      481      +27     
- Partials      298      323      +25
Files with missing lines Coverage Δ
src/spatialdata_plot/pl/render_params.py 88.10% <100.00%> (+1.34%) ⬆️
src/spatialdata_plot/pl/basic.py 86.60% <85.71%> (+0.22%) ⬆️
src/spatialdata_plot/pl/render.py 87.31% <86.46%> (+0.13%) ⬆️
src/spatialdata_plot/pl/utils.py 67.56% <70.50%> (+0.23%) ⬆️
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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@timtreis timtreis force-pushed the feature/render-graph branch 11 times, most recently from 33e1d4c to 96b07df Compare May 11, 2026 20:44
@timtreis
Add render_graph for spatial connectivity visualization
35ee4ce 
Adds sdata.pl.render_graph() to draw spatial graph edges from
adjacency matrices stored in table.obsp, using element centroids
as node positions. Supports shapes, points, and labels. Features:

- Scalar / obs-categorical / obs-continuous / obsp-matrix edge coloring
- Per-edge widths and alphas (scalar or from a weight matrix)
- Group filtering (both endpoints must be in the requested groups)
- Self-loop rendering as a CircleCollection
- Integrated colorbar via the existing ColorbarSpec pipeline
- Legend sharing with chained render_shapes / render_points
- No new dependencies (no networkx)
@timtreis timtreis force-pushed the feature/render-graph branch from 96b07df to 35ee4ce Compare May 11, 2026 20:50
@timtreis timtreis merged commit 53abe71 into main May 11, 2026
7 of 8 checks passed
@timtreis timtreis deleted the feature/render-graph branch May 11, 2026 20:58
@timtreis timtreis mentioned this pull request May 12, 2026
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