[Feature Request] Edge dry spot detection

[MicTott]

Rough workflow to Incorporate Jacqui’s Edge Dry Spot Detection into SpotSweeper.

The overall idea here is that we frequently observe edge dry spot artifacts in Visium due to incomplete reagent spread. Jacqui has developed a nice workflow that takes this edge knowledge into account to accurately detect these artifacts. So we now want to include this function into SpotSweeper.

Harriet He will be taking the lead on this.

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Preparation & Initial Setup

1. Obtain Jacqui’s existing code/functions.

2. Identify appropriate Visium samples for testing (@MicTott for help).

   • Select at least two representative Visium arrays:
     • Positive case (clear edge artifacts).
     • Negative control (clean edges).

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Development & Branching Strategy (Git Workflow)

3. Set up a new branch for feature development.

   git checkout -b feature/edge-dry-spot-detection
   git push -u origin feature/edge-dry-spot-detection

4. Incorporate Jacqui’s functions into SpotSweeper.

   • Document functions clearly (inline comments, roxygen).

5. Run local checks.

BiocCheck::BiocCheck(".")
devtools::check()

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Validation & Testing

6. Validate functions.

   • Test with selected samples.
   • Visualize via spatial plots fo validation.

7. Write unit tests (using testthat).

   • Test for output validation.

   tests/testthat/test-edge-dry-spots.R
   

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Documentation & Versioning

8. Update documentation.

   • Update README, NEWS.md clearly highlighting new feature.
   • Create new Vignette showing off the function.

9. Increment SpotSweeper version number (semantic versioning).

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Code Review & Merge

10. Open a Pull Request (PR).

• Review by @MicTott and Jacqui.

11. Merge into main after approval (@MicTott) .

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12. Push updates to GitHub/Bioconductor.

• Tag release:

git tag -a v1.4.0 -m "Release v1.4.0: Added edge dry spot detection"
git push --tags

[stephaniehicks]

Thank you @MicTott for putting this together! Hugely helpful and clear. :)