n-hop neighbors in spatial graph
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- Dominant language
- Python
- Stars
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- Avg merge
- 3d 11h
- Merged PRs (30d)
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Description
Description of feature
I think it would be useful to add a function to derive n-hop neighbors.
In some cases, that's better than just using a larger radius since it takes gaps in the tissue properly into account.
For instance, in the case of core needle biopsies, we often have situations like this one, where
(A) = cell of interest
(B) = cell of same tissue section within radius $r_1$, that's reachable via 3-hop neighborhood based on radius $r_2$.
(C) = cell on other tissue section (-> distances are not meaningful with respect to cell A) that's also within $r_1$, but cannot be reached via 3-hop neighborhood based on radius $r_2$.
IMO this would be useful irrespective of the method (radius, delauney), so probably a postprocessing function?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
The issue names no file, test, or entry point; start by reviewing Squidpy's existing radius and Delaunay spatial-neighborhood implementations. Use the A/B/C example to define n-hop reachability, and consider how a postprocessing function can work independently of the graph-construction method.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100