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feat: build Venn plots directly from DEG results - #10

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issue/venn-direct-deg-moo
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TJoshMeyer wants to merge 5 commits into
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issue/venn-direct-deg-moo

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@TJoshMeyer

@TJoshMeyer TJoshMeyer commented Aug 31, 2026 •

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Changes

  • Pass the input multiOmicDataSet directly to the Venn function instead of generating an intermediate Volcano Summary table.
  • Add significance and fold-change column/threshold controls matching the package API.
  • Keep contrast selection optional: blank uses all DEG contrasts, while a comma-separated list selects a trimmed, duplicate-free subset.
  • Remove the obsolete contrasts-column control and synchronize the vendored MOSuite Venn implementation.
  • Add contract, parser, panel, success-path, subset, and unknown-contrast tests.

Issues

Closes #11. This PR is coordinated with the companion MOSuite package PR CCBR/MOSuite#278.

Generative AI Usage Statement

GitHub Copilot in Auto mode assisted with implementation, tests, troubleshooting, commit messages, and PR preparation. The changes and diffs were manually reviewed and approved by the contributor.

PR Checklist

  • This comment contains a description of changes with justifications, with any relevant issues linked.
  • Run the capsule in Code Ocean and ensure it completes successfully with no errors.
  • Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Follow the style described in https://style.tidyverse.org/news.html
  • The tests workflow succeeds on the latest commit.

TJoshMeyer and others added 3 commits August 31, 2026 18:03
Pass the input multiOmicDataSet directly to MOSuite, expose strict DEG threshold controls, and support optional comma-separated contrast subsets.

_AI assistance: GitHub Copilot_.
_AI assistance: GitHub Copilot_.
@TJoshMeyer TJoshMeyer added the AI-assisted Changes generated with AI assistance label Aug 31, 2026
@TJoshMeyer TJoshMeyer self-assigned this Aug 31, 2026
@TJoshMeyer TJoshMeyer added the enhancement New feature or request label Aug 31, 2026
_AI assistance: GitHub Copilot_.
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Build Venn plots directly from DEG MOO results

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