feat(venn): build intersections directly from DEG results by TJoshMeyer · Pull Request #278 · CCBR/MOSuite

TJoshMeyer · 2026-08-31T22:15:12Z

Changes

Build Venn and Intersection sets directly from named per-contrast DEG results in multiOmicDataSet@analyses$diff.
Add configurable feature ID, significance, fold-change, threshold, and optional contrast-subset parameters. Blank contrast selection uses all available DEG contrasts; unknown names fail clearly.
Remove the legacy Volcano Summary data-frame method and obsolete NIDAP 1.0 Venn/Volcano Summary fixtures.
Update package documentation, report/vignette examples, and focused tests.
Remove an unstable Volcano Enhanced snapshot that asserted third-party deprecation warnings and blocked otherwise unrelated CI runs.

Issues

Closes #279. This PR is coordinated with the companion Venn capsule PR NIDAP-Community/MOSuite-plot-venn-diagram#10.

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.
Write unit tests for any new features, bug fixes, or other code changes.
Update the docs if there are any API changes (roxygen2 comments, vignettes, readme, etc.).
Update NEWS.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
Run devtools::check() locally and fix all notes, warnings, and errors.

Remove the legacy Volcano Summary data-frame path and derive Venn sets directly from per-contrast DEG results in multiOmicDataSet. _AI assistance: GitHub Copilot_.

_AI assistance: GitHub Copilot_.

Document Venn plot output controls in generated public and internal reference pages. _AI assistance: GitHub Copilot_.

Remove a snapshot that asserted third-party deprecation warnings with unstable CI behavior. _AI assistance: GitHub Copilot_.

codecov · 2026-09-02T17:02:36Z

Codecov Report

❌ Patch coverage is 89.55224% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.45%. Comparing base (1602f51) to head (c6d48b1).

Files with missing lines	Patch %	Lines
R/plot_venn_diagram.R	89.55%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #278      +/-   ##
==========================================
+ Coverage   84.06%   85.45%   +1.38%     
==========================================
  Files          24       24              
  Lines        4204     4220      +16     
==========================================
+ Hits         3534     3606      +72     
+ Misses        670      614      -56

☔ View full report in Codecov by Harness.
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TJoshMeyer · 2026-09-02T18:39:56Z

Note for reviewers:

@kelly-sovacool & @phoman14 , this PR includes one unrelated test-maintenance change:

A Volcano Enhanced console-output snapshot was flaky because it asserted deprecation warnings emitted by external packages\
The snapshot was the sole failure across the release, old-release, and coverage checks in the prior CI run
All Venn tests passed in those jobs

I removed the snapshot rather than suppressing warnings broadly, since existing tests already cover the Volcano function’s meaningful behavior.

I'd explicitly appreciate your review of my call to remove this snapshot, as I'm not sure if this was the right move or not.

TJoshMeyer · 2026-09-02T18:52:02Z

@kelly-sovacool ,

Quick local-environment question:

My focused Venn tests and installed-package report test pass, and the full GitHub CI matrix is green. However, local devtools::check() still reports one NOTE: unable to verify current time.

This appears to be a managed macOS/R environment issue rather than a package or PR #278 failure.

Do you have a recommended contributor setup or workflow for eliminating or handling this NOTE locally?

kelly-sovacool · 2026-09-02T20:11:02Z

@TJoshMeyer

Note for reviewers:

@kelly-sovacool & @phoman14 , this PR includes one unrelated test-maintenance change:

A Volcano Enhanced console-output snapshot was flaky because it asserted deprecation warnings emitted by external packages\

The snapshot was the sole failure across the release, old-release, and coverage checks in the prior CI run

All Venn tests passed in those jobs

I removed the snapshot rather than suppressing warnings broadly, since existing tests already cover the Volcano function’s meaningful behavior.

I'd explicitly appreciate your review of my call to remove this snapshot, as I'm not sure if this was the right move or not.

That was the wrong call. If there are failing tests in code unrelated to your PR, the best way forward is to investigate it in a separate branch (or ask a maintainer to do this) and not touch the code that's unrelated to your changes.

Not only were the snapshots deleted, so were the volcano package data files. Please revert all changes related to volcano tests and data. This PR should only include changes related to the venn diagram refactor.

Edited to add: "wrong call" sounds kinda harsh. The great thing about git + GitHub is: wrong calls like this are no big deal, they can be reversed! So don't sweat it.

kelly-sovacool

Please put back the deleted package data files for both venn diagram & volcano summary, and the tests related to volcano plots. This PR should only include changes related to the venn diagram refactor.

Question: is your intention that plot_venn_diagram() will create N separate venn diagram plots for each contrast?
I would suggest a different design to go about this.

calc_venn_sets method for dataframes to calculate the venn diagram information that is feed into plot_venn_sets
plot_venn_diagram method for dataframes (put this back). this accepts a dataframe and runs calc_venn_sets and plot_venn_sets.
plot_venn_diagram method for multiOmicDataSet. selects the diff dataframes depending on the contrasts input (1 or many), and formats the dataframe to feed into the plot_venn_diagram dataframe method.

kelly-sovacool · 2026-09-02T20:03:53Z

-nidap_volcano_summary_dat <- readr::read_csv(system.file(
-  "extdata",
-  "nidap",
-  "Volcano_Summary.csv.gz",
-  package = "MOSuite"
-))
-usethis::use_data(nidap_volcano_summary_dat, overwrite = TRUE)
-
-nidap_venn_diagram_dat <- readr::read_csv(system.file(
-  "extdata",
-  "nidap",
-  "Venn_Diagram.csv.gz",
-  package = "MOSuite"
-))
-usethis::use_data(nidap_venn_diagram_dat, overwrite = TRUE)
-


undo this change. these are package data that must be included. you can learn more about package data here https://r-pkgs.org/data.html

kelly-sovacool · 2026-09-02T20:04:31Z

put this file and the other nidap volcano file back. they are package data exported from NIDAP 1.0.

kelly-sovacool · 2026-09-02T20:04:54Z

-#' Summarized differential expression analysis for input to venn diagram
-#' @keywords data
-"nidap_volcano_summary_dat"
-
-#' Output data from venn diagram.
-#' The result of running `plot_venn_diagram()` on `nidap_volcano_summary_dat`
-#' @keywords data
-"nidap_venn_diagram_dat"
-


put these back too

kelly-sovacool · 2026-09-02T20:05:15Z

@@ -1,13 +1,3 @@
-test_that("plot_volcano_enhanced works on nidap dataset", {


put this back

kelly-sovacool · 2026-09-02T20:22:26Z

@TJoshMeyer

Quick local-environment question:

My focused Venn tests and installed-package report test pass, and the full GitHub CI matrix is green. However, local devtools::check() still reports one NOTE: unable to verify current time.

This appears to be a managed macOS/R environment issue rather than a package or PR #278 failure.

Do you have a recommended contributor setup or workflow for eliminating or handling this NOTE locally?

You're correct, that note is unrelated to the package code. R CMD Check tries to verify the current time (tbh I don't know why it cares) and sometimes the API to do so is unavailable -- could be the site is down, could be VPN issues on your end, could be a glitch in the matrix, etc. TLDR: this is one note that you can always safely ignore. There's probably an environment variable or something you can set if it's really bugging you.

kelly-sovacool · 2026-09-02T20:39:47Z

@TJoshMeyer I realized the whole point of the venn diagram is to compare the different contrasts, I updated my suggested design above (it's largely the same still).

Restore exported NIDAP data and unrelated Volcano test assets so the Venn PR remains scoped to its refactor. _AI assistance: GitHub Copilot_.

github-actions Bot added the MOSuite RepoName label Aug 31, 2026

TJoshMeyer added the AI-assisted label Aug 31, 2026

TJoshMeyer mentioned this pull request Aug 31, 2026

feat: build Venn plots directly from DEG results NIDAP-Community/MOSuite-plot-venn-diagram#10

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4 tasks done

TJoshMeyer self-assigned this Aug 31, 2026

TJoshMeyer added the enhancement New feature or request label Aug 31, 2026

TJoshMeyer added 4 commits September 2, 2026 11:22

feat(venn): build intersections from DEG results

46b8c34

Remove the legacy Volcano Summary data-frame path and derive Venn sets directly from per-contrast DEG results in multiOmicDataSet. _AI assistance: GitHub Copilot_.

test(venn): cover contrast subsets

7241577

_AI assistance: GitHub Copilot_.

docs: add Venn PR news entry

312c853

_AI assistance: GitHub Copilot_.

docs(venn): document output arguments

535df88

Document Venn plot output controls in generated public and internal reference pages. _AI assistance: GitHub Copilot_.

TJoshMeyer force-pushed the issue/venn-direct-deg-moo branch from f9250cf to 535df88 Compare September 2, 2026 16:04

test(volcano): remove unstable warning snapshot

c6d48b1

Remove a snapshot that asserted third-party deprecation warnings with unstable CI behavior. _AI assistance: GitHub Copilot_.

TJoshMeyer requested a review from phoman14 September 2, 2026 17:53

TJoshMeyer marked this pull request as ready for review September 2, 2026 18:52

TJoshMeyer requested a review from kelly-sovacool as a code owner September 2, 2026 18:52

kelly-sovacool requested changes Sep 2, 2026

View reviewed changes

fix(venn): restore package data and tests

834418e

Restore exported NIDAP data and unrelated Volcano test assets so the Venn PR remains scoped to its refactor. _AI assistance: GitHub Copilot_.

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feat(venn): build intersections directly from DEG results - #278

feat(venn): build intersections directly from DEG results#278
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		test_that("plot_volcano_enhanced works on nidap dataset", {

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