ci: add gha workflows from MOSuite#76
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update unit tests rev2 Update Violin Plot function to work with Layers in either Seurat v5 and below.
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* UsingClaude added Compare_Cell_Pop from NIDAPjson. passed AI tests * fixing ModScoreHelpers_function. Error with Roxygen Format * Update Vignette * Update Vignette for MS app * Start CompareCelPop Vignette * Add code for compareCellPopulations Vignette * add Vis_CCPbar.png * Render Visualizations.Rmd with pkgdown * resize CCPbar figure for vignette * Add CCPbox to Vignette * Add description for Compare Cell populations * edit CCP function description in vignette * modify ViolinPlot function name and add standard output * change violin plot name for tests violinPlot_mod -> violinPlot * Build Vignettes with updates * Modify _pkgdown.yml and /Vignevignettes/README.Rmd -> vignettes/Intro.Rmd to work with devtoools::check() * Reverting Intro.Rmd to README.Rmd * tried to troubleshoot running vignetts with devtools::check(). did not work so run devtools::check(vignettes = FALSE) * rmeove Intro.Rmd after changed to README.Rmd * add htmlttols for Vignettes * LOCAL: tried to troubleshoot running vignetts with devtools::check(). did not work so run devtools::check(vignettes = FALSE) * Modifications to pass unit tests * update vignette to use README.Rmd not Intro.Rmd * Potential fix for pull request finding Outdated, NIDAP specific function options that don't apply to Packaged function anymore. metadata.table is extracted internally Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * added Vignette docs folder * remvoed metadata.table from Compare_cell_Populations.R because no loger used (nidapism) * Initial plan * Add else-stop to getParamCCP for unknown data values Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com> * Initial plan * Add else branch to getParamCCP() with stop() for unknown datasets Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com> * adding an explicit else that stop()s with a clear message listing the supported dataset keys. * remove sptatstat.corre from DESCRIPTION * removed htmltools from DESCRIPTION * Deleted docs/reference/violinPlot_mod.html * Potential fix for pull request finding removing unused references Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding removed violinPlot_mod references Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Initial plan * Fix trailing comma in knitr chunk header in SCWorkflow-Visualizations.Rmd Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com> * Potential fix for pull request finding Metadata column validation happens before the code normalizes column names (replacing . with _ at line 158). If a caller passes annotation.column/group.column using underscores while the Seurat metadata still has dots, this will error even though the function later renames the columns. Consider normalizing object@meta.data colnames and the *.column arguments before computing missing.cols. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Potential fix for pull request finding remove violinPlot_mod Reference Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Run Tests after copiolot modifications * Potential fix for pull request finding createAnnoTable() builds cntTble by cbind()-ing unique(AnnoCol) with table(...). Because the initial matrix has numeric rownames (1..n) and table() may not return values in the same order (and can omit missing levels), this can silently misalign counts with clusters and produce an incorrect output table. Consider constructing counts with table(SO@meta.data[[AnnoCol]], SO@meta.data[[GroupCol]]) (or xtabs) so row/column names stay aligned, then compute frequencies from that matrix. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
* Update Roxygen parmameters/descriptions for Dual_Labeling
* Modify unit Tests for updated list output
* add use.assay roxygen parameter
* update unit tests for Heatmap
* add cluster.identities.table roxygen description"
* make table for cluster.identities.table when running unit tests
* modify unit tests to use plots slot instead of plot
* fixed typo param mad.topNgenes.limitsSet
* Update Test for FilterQC
* clean up vignette quotation ussaage
* Modscore change to standard output
* colorByMarkerTable-clean up function parameter layout and coment out library load
* fix Samples Bug in Plot_Metadata
* plot Metadata rearange function parameters
* Plot Metadata test error plot->plots for output
* Standardize parameters so that _->. and fix typo in parameter
* standardize parameters for inst/shiny/ModuleScoreApp
* modify test to look for plots instead of plot
* colorByGene-resolved cant find Samples error
* minor error fixes to test files to run correctly
* remove explicetly loading library in function
* return standard output list data and plot
* removue redundant use of samples to us only samples.to.include
* Harmony make standard object list of object and plots
* Harmony remove uncessary print statements
* Add title and description from .json files for Annotate_Cell_Types.R, DEG_Gene_Expression_Markers.R,Dual_Labeling.R,Filter_QC.R,Filter_Seurat_Object_by_Metadata.R
* add example function calls to roxygen section. Standardize Roxygen format between all functions
* unifiy parameter descriptions with .json files
* update documentation
* minor changes to missing packages and test not using standard output structure
* fix Violin plot not loading tidyr
* create vignettes with previous updates to variables
* make interactive plot an option for AggregateCounts
* recreate vignette
* Color_by_Genes_Automatic.R and Compare_Cell_Populations.R still did not have standard output
* Update NAMESPACE
modify pivot_longer and str_split import
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update R/Violin_Plots_by_Metadata.R
update import->importFrom for pivot_longer
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Update R/Filter_QC.R
Filter_QC.R In roxygen, square brackets [...] are interpreted as Rd links, which gets rendered as \\link{CCBR} / \\link{scRNA-seq} in the generated .Rd. Since those topics likely don't exist, this can create broken links and R CMD check warnings. Use plain text or parentheses instead (e.g., Filter Low Quality Cells (CCBR scRNA-seq)) to avoid generating invalid links.
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* Declare patchwork dependency and import plot_layout in Harmony.R (#85)
* Initial plan
* Fix patchwork::plot_layout unqualified usage in Harmony.R
Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
Agent-Logs-Url: https://github.com/NIDAP-Community/SCWorkflow/sessions/9de58a68-7e10-4304-87be-6efae85ad882
---------
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
---------
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
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