Declare patchwork dependency and import plot_layout in Harmony.R#85
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phoman14 merged 2 commits intoDEV_PhilSprintfrom Mar 26, 2026
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Declare patchwork dependency and import plot_layout in Harmony.R#85phoman14 merged 2 commits intoDEV_PhilSprintfrom
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[WIP] [WIP] Address feedback on Roxygen parameters and descriptions cleanup
Declare patchwork dependency and import plot_layout in Harmony.R
Mar 26, 2026
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Mar 26, 2026
* 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>
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Co-authored-by: phoman14 <21298645+phoman14@users.noreply.github.com>
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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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plot_layout()was called unqualified inR/Harmony.Rwithoutpatchworkdeclared as a dependency, causing a runtime error when the package is loaded withoutpatchworkattached.Changes
DESCRIPTION: AddedpatchworktoImportsR/Harmony.R: Added@importFrom patchwork plot_layoutto the roxygen blockNAMESPACE: AddedimportFrom(patchwork,plot_layout)⚡ Quickly spin up Copilot coding agent tasks from anywhere on your macOS or Windows machine with Raycast.