v2.8.5 major package update and cleanup

CITATION.cff

@@ -1,6 +1,6 @@
 cff-version: 1.2.0
 title: vertesy/Seurat.utils
-version: v2.8.0
+version: v2.8.5
 message: >-
   If you use this software, please cite it using these metadata.
 type: software

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat.utils
 Title: Seurat.utils - utility functions for Seurat
-Version: 2.8.0
+Version: 2.8.5
 Authors@R: 
     person("Abel", "Vertesy", , "[email protected]", role = c("aut", "cre"))
 Author: Abel Vertesy <[email protected]> [aut, cre]
@@ -14,21 +14,26 @@ BugReports: https://github.com/vertesy/Seurat.utils/issues
 Depends: 
     CodeAndRoll2,
     ggExpress,
-    ggplot2,
     magrittr,
     Seurat,
-    Stringendo
+    Stringendo,
+    tidyverse
 Imports: 
+    checkmate,
     cowplot,
     dplyr,
+    EnhancedVolcano,
     foreach,
+    fs,
+    future,
     ggcorrplot,
+    ggplot2,
     ggpubr,
     ggrepel,
-    grDevices,
+    gplots,
+    harmony,
     HGNChelper,
     htmlwidgets,
-    job,
     MarkdownHelpers,
     MarkdownReports,
     Matrix,
@@ -38,27 +43,24 @@ Imports:
     princurve,
     qs,
     R.utils,
+    RColorBrewer,
     readr,
     ReadWriter,
     reshape2,
     rstudioapi,
     scales,
+    SeuratObject,
     SoupX,
     sparseMatrixStats,
     stringr,
     tibble,
-    tictoc,
-    tidyverse,
-    vroom
+    tictoc
 Suggests: 
+    clusterProfiler,
     DatabaseLinke.R,
-    EnhancedVolcano,
-    fs,
-    gplots,
-    princurve,
-    RColorBrewer,
-    SoupX
+    enrichplot,
+    vroom
 Encoding: UTF-8
-Packaged: 2024-06-21 12:31:42.585143
+Packaged: 2024-10-23 22:59:23.332565
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1

Development/Create_the_Seurat.utils_Package.R

@@ -1,7 +1,8 @@
 ######################################################################################################
 # Create_the_Seurat.utils_Package.R
 ######################################################################################################
-# source("~/GitHub/Packages/Seurat.utils/Development/Create_the_Seurat.utils_Package.R")
+# file.edit("~/GitHub/Packages/Seurat.utils/Development/Create_the_Seurat.utils_Package.R")
+
 # rm(list = ls(all.names = TRUE));
 try(dev.off(), silent = TRUE)
 
@@ -20,8 +21,11 @@ file.edit(config.path)
 source(config.path)
 package.name <- DESCRIPTION$'package.name'
 
+
+
 PackageTools::document_and_create_package(repository.dir, config_file = 'config.R')
 'git add commit push to remote'
+file.edit("DESCRIPTION")
 
 # Install your package ------------------------------------------------
 "disable rprofile by"
@@ -47,11 +51,13 @@ devtools::install_github(repo = "vertesy/Seurat.utils", upgrade = F)
 # BiocManager::install("MatrixGenerics")
 
 # CMD CHECK ------------------------------------------------
+devtools::check_man(repository.dir)
 checkres <- devtools::check(repository.dir, cran = FALSE)
 
 
 # Automated Codebase linting to tidyverse style ------------------------------------------------
 styler::style_pkg(repository.dir)
+# styler::style_file("~/GitHub/Packages/Seurat.utils/R/Seurat.Utils.Visualization.R")
 
 
 # Extract package dependencies ------------------------------------------------
@@ -69,7 +75,7 @@ PackageTools::extract_package_dependencies(repository.dir)
 
 # Try to find and add missing @importFrom statements------------------------------------------------
 devtools::load_all("~/GitHub/Packages/PackageTools/")
-(ls.scripts.full.path <- list.files(file.path(repository.dir, "R"), full.names = T))
+(ls.scripts.full.path <- list.files(file.path(repository.dir, "R"), full.names = T, pattern = ".R$"))
 if (F) {
   (excluded.packages <- unlist(strsplit(DESCRIPTION$'depends', split = ", ")))
   for (scriptX in ls.scripts.full.path) {
@@ -78,6 +84,7 @@ if (F) {
 }
 
 # Replaces T with TRUE and F with FALSE ------------------------------------------------
+(ls.scripts.full.path <- list.files(file.path(repository.dir, "R"), full.names = T, pattern = ".R$"))
 for (scriptX in ls.scripts.full.path) {
   PackageTools::replace_tf_with_true_false(scriptX, strict_mode = F)
   PackageTools::replace_short_calls(scriptX, strict_mode = F)

Development/config.R

@@ -1,19 +1,21 @@
 # Configuration for the Package
 DESCRIPTION <- list(
   package.name = "Seurat.utils",
-  version = "2.8.0",
+  version = "2.8.5",
   title = "Seurat.utils - utility functions for Seurat",
   description = "Seurat.utils Is a collection of utility functions for Seurat single cell analysis.
     Functions allow 3D plotting, visualisation of statistics & QC,
     the automation / multiplexing of plotting, interaction with the Seurat object, etc.
     Some functionalities require functions from CodeAndRoll and MarkdownReports libraries.",
-  depends = "ggplot2, Seurat, Stringendo, CodeAndRoll2, ggExpress, magrittr",
-  imports = "cowplot, ReadWriter, dplyr, ggcorrplot, ggpubr, ggrepel, grDevices, HGNChelper,
-    htmlwidgets, MarkdownHelpers, MarkdownReports, Matrix, matrixStats, princurve, pheatmap,
+  depends = "tidyverse, Seurat, Stringendo, CodeAndRoll2, ggExpress, magrittr",
+  imports = "cowplot, dplyr, ggcorrplot, ggpubr, ggrepel, HGNChelper, htmlwidgets,
+    Matrix, matrixStats, princurve, pheatmap,
     R.utils, readr, reshape2, scales, SoupX, sparseMatrixStats, stringr, tibble, tictoc,
-    plotly, rstudioapi, vroom, job, qs, foreach, tidyverse",
-  suggests = "SoupX, princurve, EnhancedVolcano, DatabaseLinke.R, RColorBrewer, fs, gplots",
-
+    ReadWriter, MarkdownHelpers, MarkdownReports,
+    plotly, qs, foreach, harmony, EnhancedVolcano, rstudioapi,
+    RColorBrewer, SeuratObject, checkmate, fs, future,
+    ggplot2, gplots", # , grDevices
+  suggests = "clusterProfiler, enrichplot, DatabaseLinke.R, vroom", #, job
   author.given = "Abel",
   author.family = "Vertesy",
   author.email = "[email protected]",

NAMESPACE

@@ -193,17 +193,14 @@ export(ww.get.1st.Seur.element)
 export(xread)
 export(xsave)
 import(Seurat)
-import(enrichplot)
 import(tidyverse)
 importFrom(CodeAndRoll2,as_tibble_from_namedVec)
 importFrom(CodeAndRoll2,clip.outliers.at.percentile)
 importFrom(CodeAndRoll2,df.col.2.named.vector)
 importFrom(CodeAndRoll2,grepv)
 importFrom(CodeAndRoll2,translate)
-importFrom(DatabaseLinke.R,qHGNC)
 importFrom(EnhancedVolcano,EnhancedVolcano)
 importFrom(HGNChelper,checkGeneSymbols)
-importFrom(MarkdownHelpers,color_check)
 importFrom(MarkdownHelpers,llogit)
 importFrom(MarkdownHelpers,llprint)
 importFrom(MarkdownHelpers,ww.assign_to_global)
@@ -249,7 +246,6 @@ importFrom(Seurat,ScaleData)
 importFrom(Seurat,TransferData)
 importFrom(Seurat,VariableFeatures)
 importFrom(SeuratObject,UpdateSeuratObject)
-importFrom(SoupX,SoupChannel)
 importFrom(Stringendo,iprint)
 importFrom(Stringendo,kollapse)
 importFrom(Stringendo,kpp)
@@ -258,7 +254,6 @@ importFrom(Stringendo,percentage_formatter)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_class)
 importFrom(checkmate,assert_string)
-importFrom(clusterProfiler,enrichGO)
 importFrom(cowplot,ggdraw)
 importFrom(cowplot,ggsave2)
 importFrom(cowplot,plot_grid)
@@ -314,8 +309,8 @@ importFrom(ggrepel,geom_text_repel)
 importFrom(gplots,rich.colors)
 importFrom(graphics,par)
 importFrom(graphics,text)
+importFrom(harmony,RunHarmony)
 importFrom(htmlwidgets,saveWidget)
-importFrom(job,job)
 importFrom(matrixStats,rowSums2)
 importFrom(pheatmap,pheatmap)
 importFrom(plotly,layout)
@@ -341,4 +336,3 @@ importFrom(tibble,rownames_to_column)
 importFrom(tictoc,tic)
 importFrom(tictoc,toc)
 importFrom(tools,toTitleCase)
-importFrom(vroom,vroom)