feat: create fetch_celldex_ref() and label significant genes in make_volcano_plot() by wong-nw · Pull Request #21 · CCBR/SCOT

wong-nw · 2025-11-14T20:10:41Z

Changes

Updates to volcano plot to identify number of significant genes or list of genes to label on plot
Includes updated function fetch_celldex_ref to create local cache in working directory to retrieve celldex references for celltype annotation
Updates singleR function calls to use fetch_celldex_ref
Includes unit tests for run_singleR.R and run_singleR_cluster
- Includes helper function for retrieving pbmc dataset from SeuratData for testing

Issues

Slowly addressing create unit tests #10
Working through Feature Checklist #2
Correcting through use package::function() syntax #17 as we go.

PR Checklist

(~~Strikethrough~~ any points that are not applicable.)

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.

Merge main into Nathan

kelly-sovacool

See my comments for problems that will need to be addressed.

Please run devtools::check() after you've made the changes and ensure there are no errors or warnings.

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

Using `package::function()` format

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

https://github.com/CCBR/SCOT/actions/runs/19504260134/job/55826111606\#step:6:12

* fix: package function calling * Update helper function * ci: 🤖 auto-format --------- Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Corrects issue with `Idents` function

kelly-sovacool · 2025-12-02T19:17:26Z

new test failures

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-run_singleR_cluster.R:24:3'): cluster_cell_annot_type_count ──
Expected `length(which(singleR_cluster == "B_cell"))` to equal 345.
Differences:
  `actual`: 347.0
`expected`: 345.0

── Failure ('test-run_singleR_cluster.R:25:3'): cluster_cell_annot_type_count ──
Expected `length(which(singleR_cluster == "Monocyte"))` to equal 672.
Differences:
  `actual`: 671.0
`expected`: 672.0

── Failure ('test-run_singleR_cluster.R:26:3'): cluster_cell_annot_type_count ──
Expected `length(which(singleR_cluster == "NK_cell"))` to equal 157.
Differences:
  `actual`: 155.0
`expected`: 157.0

── Failure ('test-run_singleR_cluster.R:27:3'): cluster_cell_annot_type_count ──
Expected `length(which(singleR_cluster == "T_cells"))` to equal 1452.
Differences:
  `actual`: 1453.0
`expected`: 1452.0


[ FAIL 4 | WARN 697 | SKIP 0 | PASS 61 ]
Error:
! Test failures.
Execution halted

1 error ✖ | 1 warning ✖ | 1 note ✖

@wong-nw can you try running check() locally and make sure everything is addressed?

kelly-sovacool · 2025-12-05T16:26:23Z

@wong-nw did devtools::check() pass locally in a fresh R session? it's still failing via github actions.

── R CMD check results ──────────────────────────────────── SCOT 0.0.0.9000 ────
Duration: 14m 48s

❯ checking dependencies in R code ... WARNING
  Namespaces in Imports field not imported from:
    ‘harmony’ ‘rliger’ ‘stats’
    All declared Imports should be used.
  Missing or unexported object: ‘SeuratData::DefaultAssay<-’

❯ checking R code for possible problems ... NOTE
  cluster_metrics: no visible global function definition for ‘dist’
    (/home/runner/work/SCOT/SCOT/check/SCOT.Rcheck/00_pkg_src/SCOT/R/cluster_metrics.R:42)
  run_batch_correction: no visible binding for global variable
    ‘scVIIntegration’
    (/home/runner/work/SCOT/SCOT/check/SCOT.Rcheck/00_pkg_src/SCOT/R/run_batch_correction.R:71-77)
  run_hypergeometric_test: no visible global function definition for
    ‘phyper’
    (/home/runner/work/SCOT/SCOT/check/SCOT.Rcheck/00_pkg_src/SCOT/R/run_hypergeometric_test.R:35-41)
  Undefined global functions or variables:
    dist phyper scVIIntegration
  Consider adding
    importFrom("stats", "dist", "phyper")
  to your NAMESPACE file.

Error: Error: R CMD check found WARNINGs
Execution halted
0 errors ✔ | 1 warning ✖ | 1 note ✖

Looks like there are still functions that need to be called with package::function() syntax:
- stats::dist()
- stats::phyper()
- scVIIntegration -- is that from harmony or rliger?
If any packages in imports are not actually used, they need to be removed.

Please make these fixes, restart your R session, then run devtools::check() to ensure there are no errors or warnings.

kelly-sovacool

#21 (comment)

wong-nw and others added 6 commits November 13, 2025 14:25

Merge pull request #20 from CCBR/main

9a0390f

Merge main into Nathan

feat: tests and plotting function updates

d708f7c

Update make_volcano_plot.R

20fdc00

Update make_volcano_plot.R

c576bf5

chore: resolve DESCRIPTION merge conflict

2540e55

feat: update singleR commands

c3a5d4a

wong-nw requested a review from kelly-sovacool November 14, 2025 20:10

github-actions Bot added the SCOT RepoName label Nov 14, 2025

kelly-sovacool requested changes Nov 18, 2025

View reviewed changes

Comment thread R/fetch_celldex_ref.R Outdated

wong-nw and others added 6 commits November 18, 2025 11:13

Apply suggestions from code review

40c6ad0

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

fix: update to correct errors in PR

ee6cbfb

fix: merge conflict resolution

9d3470e

fix: updates for check log

0af99b0

Update helper.R

606080d

Using `package::function()` format

Update R/fetch_celldex_ref.R

b8ee336

Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>

wong-nw requested a review from kelly-sovacool November 18, 2025 18:18

fix: typo

662ab6a

kelly-sovacool changed the title ~~PR: Code updates~~ feat: create fetch_celldex_ref() and label significant genes in make_volcano_plot() Nov 18, 2025

kelly-sovacool and others added 4 commits November 18, 2025 14:36

chore: document()

dbc2377

fix: documentation; feat: scale in bubble plot

683c85c

ci: 🤖 auto-format

c48a855

style: fix lint errors

1259d31

https://github.com/CCBR/SCOT/actions/runs/19504260134/job/55826111606\#step:6:12

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