New fun compare cel pop

[phoman14]

Created compareCellPopulations function from /inst/extdata/NIDAPjson/Compare_Cell_Populations.code-template.json
1)Added Roxygen documentation
2)created unit tests and Helper funcitions
3)Updated Vignette vignettes/SCWorkflow-Visualizations.Rmd
4)passed tests on for R 4.1.3 ON RStudio Workbench
1) restart R
2) .libPaths(c("/home/homanpj/R/x86_64-pc-linux-gnu-library/4.1",
"/opt/R/4.1.3/lib64/R/library",
"/rstudio-files/ccbr-data/renv_cache/single-cell-rna-seq-r4/Snapshot-environment_method/renv/library/R-4.1/x86_64-pc-linux-gnu"))
3)library(spatstat.core)
4)library(Seurat)
5)load_all()

[Copilot]

Pull request overview

This PR adds a new compareCellPopulations() visualization utility to SCWorkflow (with documentation and tests), updates vignettes/pkgdown site outputs, and renames/updates the violin plotting API used in docs and tests.

Changes:

• Add compareCellPopulations() (R implementation + Rd) and a new snapshot-based test suite with helpers.
• Rename violinPlot_mod() → violinPlot() and update vignette/test call sites.
• Update vignettes and committed pkgdown site artifacts (docs/) to surface new functions and workflow content.

Reviewed changes

Copilot reviewed 41 out of 46 changed files in this pull request and generated 24 comments.

Show a summary per file

File	Description
vignettes/SCWorkflow-Visualizations.Rmd	Update violin plot call + add Compare Cell Populations vignette section
vignettes/SCWorkflow-Usage.Rmd	Fix vignette index entry
vignettes/SCWorkflow-QC.Rmd	Fix vignette index entry
vignettes/SCWorkflow-DEG.Rmd	Add magrittr import in vignette
vignettes/SCWorkflow-Annotations.Rmd	Add magrittr import in vignette
vignettes/README.Rmd	Convert README vignette metadata to html_vignette (“Intro”)
tests/testthat/test-Violin_Plots_by_Metadata.R	Switch tests to call violinPlot()
tests/testthat/test-Compare_Cell_Populations.R	Add new compareCellPopulations test coverage + snapshots
tests/testthat/helper-Compare_Cell_Populations.R	Add test parameter builder + snapshot helpers
man/violinPlot.Rd	Rename Rd topic to violinPlot and update args (layer)
man/modscore-imports.Rd	Add internal imports topic for ModuleScore helpers
man/modscore-imports-011726.Rd	Add internal imports topic for ModuleScore helpers (dated variant)
man/modScore.Rd	Document new group_var argument
man/launch_module_score_app.Rd	Add Rd for launching ModuleScore Shiny app
man/compareCellPopulations.Rd	Add Rd for compareCellPopulations
inst/extdata/NIDAPjson/Compare_Cell_Populations.code-template.json	Add NIDAP JSON template source for CCP
docs/sitemap.xml	Update sitemap entries for new pages
docs/reference/violinPlot_mod.html	Update legacy violinPlot_mod reference HTML (still present)
docs/reference/object.html	Add examples section in reference HTML
docs/reference/modScore.html	Update usage/examples for group_var
docs/reference/index.html	Add new function links in reference index
docs/reference/colorByMarkerTable.html	Update args/examples in reference HTML
docs/pkgdown.yml	Update pkgdown site config (articles list, timestamps)
docs/index.html	Add “Key Functions” section + license link changes
docs/authors.html	Update citation year
docs/articles/index.html	Update article index links (Intro)
docs/articles/SCWorkflow-Visualizations.html	Rendered vignette includes CCP section + updated violin plot call
docs/articles/SCWorkflow-Overview.html	Remove old overview article (HTML deleted)
docs/articles/SCWorkflow-DEG.html	Update rendered vignette links (aggregateCounts)
docs/LICENSE-text.html	Update rendered license text output
docs/CHANGELOG.html	Update rendered changelog with v1.0.3 notes
README.md	Add “Key Functions” section
R/Violin_Plots_by_Metadata.R	Rename function to violinPlot, switch slot→layer, change return value
R/ModuleScoreHelpers_011726.R	Add roxygen import topic + importFrom fixes
R/ModuleScoreHelpers.R	Add roxygen import topic + importFrom fixes
R/Compare_Cell_Populations.R	Add new compareCellPopulations implementation
NAMESPACE	Export new functions and rename violin export
DESCRIPTION	Add dependencies for new functionality
CHANGELOG.md	Add v1.0.3 notes
.gitignore	Ignore doc/ and Meta/
.Rbuildignore	Ignore doc and Meta

Comments suppressed due to low confidence (2)

tests/testthat/test-Violin_Plots_by_Metadata.R:13

• violin_test is used as if it were a ggplot (passed to .drawViolin() and checked for ggplot class), but violinPlot() currently returns a list (list(plots=...)). Update the tests to use violin_test$plots (and adjust the class assertion accordingly), or revert violinPlot() to return a ggplot.
  docs/pkgdown.yml:7
• docs/pkgdown.yml declares an Intro: Intro.html article, but docs/articles/Intro.html is not present in this PR. This will break the pkgdown site navigation; either regenerate pkgdown so the article is emitted, or remove/rename the entry to match the committed HTML output.

articles:
  CONTRIBUTING: CONTRIBUTING.html
  README: README.html
  SCWorkflow-Annotations: SCWorkflow-Annotations.html

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[phoman14]

Changes look correct. The correct files were modified. unit tests were created and Vignette files appropriately updated

[Copilot]

@phoman14 I've opened a new pull request, #81, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@phoman14 I've opened a new pull request, #82, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@phoman14 I've opened a new pull request, #83, to work on those changes. Once the pull request is ready, I'll request review from you.