Clean up Roxygen parametrs and descriptions

[phoman14]

General clean up of Roxygen parameters

1. make sure parameters use . not _
2. add missing parameters
3. remove unused parameters
4. add missing function descriptions
5. add example usage

Run Full tests and fix errors
most modifications were for improper use of outputs (object,plots,data)

Update Vignettes with parameter changes

[Copilot]

Pull request overview

This PR standardizes function parameter naming in Roxygen docs (favoring . over _), aligns returned object structures (e.g., plots/data) across functions and tests, and refreshes vignettes/pkgdown artifacts accordingly.

Changes:

• Updated multiple APIs/docs/tests to consistently use dotted parameter names and plots/data outputs.
• Added/expanded Roxygen examples and value sections for several exported functions.
• Regenerated pkgdown site + vignette assets to reflect the updated documentation and outputs.

Reviewed changes

Copilot reviewed 102 out of 302 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
vignettes/images/Vis_3D_files/crosstalk-1.2.0/scss/crosstalk.scss	Adds vendored SCSS asset under vignette images output
vignettes/images/Vis_3D_files/crosstalk-1.2.0/css/crosstalk.min.css	Adds vendored minified CSS asset under vignette images output
vignettes/SCWorkflow-Visualizations.Rmd	Updates parameter naming/examples in visualization vignette
vignettes/SCWorkflow-SubsetReclust.Rmd	Updates parameter naming/examples and minor formatting
vignettes/SCWorkflow-QC.Rmd	Updates parameter naming/examples for QC workflow
vignettes/SCWorkflow-Annotations.Rmd	Updates/guards external annotation section and parameter naming
tests/testthat/test-Violin_Plots_by_Metadata.R	Updates tests to use violin_test$plots
tests/testthat/test-Recluster_Seurat_Object.R	Updates expected output names from plot to plots
tests/testthat/test-Plot_Metadata.R	Updates expected output names from plot to plots
tests/testthat/test-Name_Clusters_by_Enriched_Cell_Type.R	Updates expected output names and metadata column casing/assertions
tests/testthat/test-ModuleScore.R	Updates argument names (ms.threshold, use.columns) in tests/comments
tests/testthat/test-Heatmap.R	Updates expected output name from plot to plots
tests/testthat/test-Harmony.R	Comments out all Harmony tests
tests/testthat/test-Filter_Seurat_Object_by_Metadata.R	Updates expected output structure to plots
tests/testthat/test-Filter_QC.R	Updates expected element names (FilteringTables → data)
tests/testthat/test-Dual_Labeling.R	Updates expected output structure to nested plots/data
tests/testthat/test-Dotplot_by_Metadata.R	Updates expected output structure to plots/data
tests/testthat/test-DEG_Gene_Expression_Markers.R	Updates expected output name (df → data)
tests/testthat/test-Color_by_Gene.R	Updates expected output structure (plot → plots, object → data)
tests/testthat/test-Annotate_Cell_Types.R	Updates expected output structure to plots
tests/testthat/test-AggregateCounts.R	Updates tests to expect res$data
tests/testthat/test-3D_tSNE.R	Updates expected output name (plot → plots)
tests/testthat/helper-Violin_Plots_by_Metadata.R	Updates helper arg names to dotted variants
tests/testthat/helper-Name_Clusters_by_Enriched_Cell_Type.R	Introduces cluster.identities.table mapping helper
tests/testthat/helper-ModuleScore.R	Updates helper arg names to dotted variants
tests/testthat/helper-Filter_QC.R	Adds do.doublets.filter to helper params
test_workflow_from_Harmony.R	Updates parameter naming in workflow script
man/violinPlot.Rd	Updates documented parameter names to dotted variants
man/tSNE3D.Rd	Adds \value{} and examples
man/processRawData.Rd	Adds examples
man/plotMetadata.Rd	Adds examples
man/nameClusters.Rd	Updates usage order/docs and adds examples
man/modscore-imports.Rd	Documents compute_modscore_data() and adds examples
man/modScore.Rd	Renames args (group.var, use.columns, ms.threshold) and updates docs/examples
man/heatmapSC.Rd	Renames use.assay and updates row.order docs/examples
man/harmonyBatchCorrect.Rd	Fixes Rd topic/name/usage and argument docs
man/filterSeuratObjectByMetadata.Rd	Updates title/description and adds examples
man/filterQC.Rd	Renames args (n.topgenes, do.doublets.filter, vars.to.regress) and adds docs/examples
man/dualLabeling.Rd	Updates title/description, expands args, adds examples
man/dotPlotMet.Rd	Adds examples
man/degGeneExpressionMarkers.Rd	Updates title/description and adds examples
man/combineNormalize.Rd	Adds examples
man/colorByGene.Rd	Adds examples
man/annotateCellTypes.Rd	Updates title/description and adds examples
man/aggregateCounts.Rd	Updates usage/args and adds examples
inst/shiny/ModuleScoreApp/app_011726.R	Renames inputs/args to dotted variants (step.size, group.var, etc.)
inst/shiny/ModuleScoreApp/app.R	Renames inputs/args to dotted variants (step.size, group.var, etc.)
docs/sitemap.xml	Updates published site links
docs/reference/violinPlot.html	Regenerated pkgdown reference reflecting dotted args
docs/reference/tSNE3D.html	Regenerated pkgdown reference with value/examples
docs/reference/processRawData.html	Regenerated pkgdown reference with examples
docs/reference/plotMetadata.html	Regenerated pkgdown reference with examples
docs/reference/nameClusters.html	Regenerated pkgdown reference with updated usage/docs
docs/reference/modscore-imports.html	Regenerated pkgdown page incl. compute_modscore_data()
docs/reference/modScore.html	Regenerated pkgdown reference reflecting renamed args
docs/reference/index.html	Regenerated pkgdown index including harmonyBatchCorrect
docs/reference/heatmapSC.html	Regenerated pkgdown reference reflecting renamed args
docs/reference/harmonyBatchCorrect.html	Adds pkgdown page for harmonyBatchCorrect
docs/reference/filterSeuratObjectByMetadata.html	Regenerated pkgdown reference reflecting new title/desc/examples
docs/reference/filterQC.html	Regenerated pkgdown reference reflecting renamed args/examples
docs/reference/dotPlotMet.html	Regenerated pkgdown reference with examples
docs/reference/degGeneExpressionMarkers.html	Regenerated pkgdown reference with examples
docs/reference/compute_modscore_data.html	Adds redirect page for compute_modscore_data
docs/reference/compareCellPopulations.html	Updates usage/docs ordering (metadata.table removed)
docs/reference/combineNormalize.html	Regenerated pkgdown reference with examples
docs/reference/colorByGene.html	Regenerated pkgdown reference with examples
docs/reference/annotateCellTypes.html	Regenerated pkgdown reference with updated title/desc/examples
docs/reference/aggregateCounts.html	Regenerated pkgdown reference reflecting new args/examples
docs/pkgdown.yml	Updates last_built timestamp
docs/articles/SCWorkflow-SubsetReclust.html	Regenerated article reflecting parameter string updates
docs/articles/SCWorkflow-QC.html	Regenerated article reflecting renamed args
R/Violin_Plots_by_Metadata.R	Renames parameters to dotted variants and adjusts implementation accordingly
R/Process_Raw_Data.R	Adds Roxygen examples
R/Plot_Metadata.R	Adds examples and adjusts sample parsing logic
R/Name_Clusters_by_Enriched_Cell_Type.R	Changes API to accept cluster mapping table + adds examples
R/ModuleScoreHelpers_011726.R	Renames args to dotted variants (marker.list, use.columns, group.var)
R/ModuleScoreHelpers.R	Renames args to dotted variants and adds examples
R/Heatmap.R	Renames use.assay and updates docs + internal selection logic
R/Harmony.R	Renames args, removes library() calls, changes return to include plots
R/Filter_Seurat_Object_by_Metadata.R	Updates title/description and adds examples
R/Filter_QC.R	Renames args (n.topgenes, do.doublets.filter, vars.to.regress) + adds examples
R/Dual_Labeling.R	Updates docs + return object structure by reduction type
R/Dotplot_by_Metadata.R	Adds examples and import tags
R/DEG_Gene_Expression_Markers.R	Updates title/description and adds examples
R/Combine_and_Normalize.R	Adds examples
R/Color_by_Genes_Automatic.R	Removes inline library() calls and reformats signature
R/Color_by_Gene.R	Adds examples and fixes sample parsing variable usage
R/Annotate_Cell_Types.R	Updates title/description and adds examples
R/AggregateCounts.R	Adds interactive option and changes return to list(data,plots)
R/3D_tSNE.R	Adds @return + examples
NAMESPACE	Exports harmonyBatchCorrect; updates imports (some invalid)
.Rhistory	Updates example calls (should not be committed)

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[Copilot]

@phoman14 I've opened a new pull request, #85, 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, #86, to work on those changes. Once the pull request is ready, I'll request review from you.