Merge pull request #81 from samuel-marsh/release/1.1.0

Release 1.1.0

.Rbuildignore

@@ -11,3 +11,7 @@
 ^\.github$
 vignettes/*.orig$
 ^vignettes$
+^index\.Rmd$
+^README\.Rmd$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          upload-results: true

.gitignore

@@ -8,3 +8,4 @@ vignettes/assets
 README.Rmd
 index.Rmd
 figure/
+vignettes/articles/assets

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 1.1.0
+Date: 2022-12-22 21:24:58 UTC
+SHA: f0aff7dee2b0af306b2a055748640c8b31ccdebc

DESCRIPTION

@@ -1,71 +1,69 @@
 Package: scCustomize
 Type: Package
-Title: An R package for custom visualization & analyses of single cell sequencing.
-Version: 1.0.2
-Date: 2022-11-22
+Title: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing
+Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'.  'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions.  For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430>.
+Version: 1.1.0
+Date: 2022-12-22
 Authors@R: c(
     person(given = "Samuel", family = "Marsh", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")),
     person(given = "Ming", family = "Tang", role = c("ctb"), email = "[email protected]"),
     person(given = 'Velina', family = 'Kozareva', role = c('ctb')),
-    person(given = "Tim", family = "Stuart", email = "tstuart@nygenome.org", role = "ctb")
+    person("Lucas", "Graybuck", email = "lucasg@alleninstitute.org", role = c('ctb'))
     )
-Description: Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
-URL: https://github.com/samuel-marsh/scCustomize, https://samuel-marsh.github.io/scCustomize, https://doi.org/10.5281/zenodo.5706431
+URL: https://cran.r-project.org/package=scCustomize https://github.com/samuel-marsh/scCustomize, https://samuel-marsh.github.io/scCustomize/, https://doi.org/10.5281/zenodo.5706431
 BugReports: https://github.com/samuel-marsh/scCustomize/issues
 Depends: R (>= 4.0.0),
          Seurat (>= 4.3.0)
 Imports: 
     circlize,
     cli (>= 3.2.0),
-    colorway (>= 0.2.0),
     cowplot,
     data.table,
     dplyr,
     forcats,
     ggbeeswarm,
     ggplot2,
-    ggpubr,
     ggprism,
     ggrastr,
     ggrepel,
     glue,
+    grDevices,
     grid,
     janitor,
+    lifecycle,
     magrittr,
     Matrix (>= 1.5.0),
+    methods,
     paletteer,
     patchwork,
     pbapply,
     purrr,
-    remotes (>= 2.4.0),
     rlang (>= 1.0.1),
     scales,
     scattermore (>= 0.7), 
-    Seurat (>= 4.2.0),
     SeuratObject (>= 4.1.2),
+    stats,
     stringi,
     stringr,
     tibble,
     tidyr,
-    tidyselect,
     viridis
-Remotes: 
-    hypercompetent/colorway,
-    csdaw/ggprism
 Suggests:
     ComplexHeatmap,
     dittoSeq,
     DropletUtils,
+    ggpubr,
     hdf5r,
     knitr,
     Nebulosa,
+    remotes,
     rliger,
     rmarkdown,
+    tidyselect,
     tidyverse, 
     qs
-VignetteBuilder: knitr, rmarkdown
-License: GPL (>= 3) | file LICENSE
+License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3

NAMESPACE

@@ -11,6 +11,7 @@ export(Blank_Theme)
 export(Case_Check)
 export(CellBender_Diff_Plot)
 export(CellBender_Feature_Diff)
+export(Cell_Highlight_Plot)
 export(Change_Delim_All)
 export(Change_Delim_Prefix)
 export(Change_Delim_Suffix)
@@ -30,9 +31,11 @@ export(DimPlot_LIGER)
 export(DimPlot_scCustom)
 export(DiscretePalette_scCustomize)
 export(DotPlot_scCustom)
+export(Extract_Sample_Meta)
 export(Extract_Top_Markers)
 export(FeaturePlot_DualAssay)
 export(FeaturePlot_scCustom)
+export(Fetch_Meta)
 export(Gene_Present)
 export(Hue_Pal)
 export(Iterate_Cluster_Highlight_Plot)
@@ -128,9 +131,11 @@ import(Matrix)
 import(Seurat)
 import(cli)
 import(ggplot2)
+import(ggrastr)
 import(parallel)
 import(patchwork)
 import(pbapply)
+import(rlang)
 import(viridis)
 importFrom(Matrix,readMM)
 importFrom(Matrix,rowSums)
@@ -147,39 +152,50 @@ importFrom(Seurat,VariableFeaturePlot)
 importFrom(Seurat,VizDimLoadings)
 importFrom(Seurat,VlnPlot)
 importFrom(SeuratObject,DefaultDimReduc)
+importFrom(SeuratObject,PackageCheck)
 importFrom(circlize,colorRamp2)
-importFrom(colorway,varibow)
 importFrom(cowplot,theme_cowplot)
 importFrom(data.table,fread)
+importFrom(dplyr,all_of)
+importFrom(dplyr,any_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,desc)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,grouped_df)
 importFrom(dplyr,intersect)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,one_of)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,select_at)
 importFrom(dplyr,slice)
 importFrom(dplyr,slice_max)
 importFrom(dplyr,summarise_at)
+importFrom(dplyr,summarize)
 importFrom(forcats,fct_relevel)
 importFrom(ggbeeswarm,geom_quasirandom)
 importFrom(ggplot2,theme)
 importFrom(ggprism,theme_prism)
-importFrom(ggpubr,stat_compare_means)
 importFrom(ggrepel,geom_label_repel)
 importFrom(ggrepel,geom_text_repel)
 importFrom(glue,glue_collapse)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,pdf)
+importFrom(grDevices,rainbow)
 importFrom(grid,gpar)
 importFrom(grid,grid.circle)
 importFrom(grid,grid.rect)
 importFrom(janitor,adorn_totals)
+importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
+importFrom(methods,as)
 importFrom(methods,new)
+importFrom(methods,slot)
 importFrom(paletteer,paletteer_d)
 importFrom(patchwork,plot_annotation)
 importFrom(patchwork,plot_layout)
@@ -194,10 +210,17 @@ importFrom(purrr,map2)
 importFrom(purrr,map_dbl)
 importFrom(purrr,pluck)
 importFrom(purrr,reduce)
+importFrom(rlang,sym)
 importFrom(scales,alpha)
 importFrom(scales,hue_pal)
 importFrom(scales,label_percent)
 importFrom(scattermore,geom_scattermore)
+importFrom(stats,cor)
+importFrom(stats,kmeans)
+importFrom(stats,median)
+importFrom(stats,quantile)
+importFrom(stats,setNames)
+importFrom(stats,var)
 importFrom(stringi,stri_replace_first_fixed)
 importFrom(stringi,stri_replace_last_fixed)
 importFrom(stringr,str_detect)
@@ -210,9 +233,11 @@ importFrom(tibble,rownames_to_column)
 importFrom(tibble,tribble)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,pivot_wider)
-importFrom(tidyselect,all_of)
 importFrom(utils,combn)
 importFrom(utils,packageVersion)
+importFrom(utils,read.csv)
 importFrom(utils,read.delim)
+importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
+importFrom(utils,write.csv)

NEWS.md

@@ -1,3 +1,24 @@
+# scCustomize 1.1.0 (2022-12-22)  
+## Added  
+- Added `merge` parameter to `Read10X_GEO`, `Read10X_h5_GEO`, `Read_GEO_Delim` and `Read_CellBender_h5_Multi_File`.  
+- Added `raster.dpi` parameter to `DimPlot_LIGER`.  
+- Added `label` parameter to `FeaturePlot_scCustom` to avoid error collision ([#80](https://github.com/samuel-marsh/scCustomize/issues/80)).  
+- Added `vln_linewidth` parameter to control violin outline line width ([#32](https://github.com/samuel-marsh/scCustomize/issues/32)).  
+- Added quick meta data getter function `Fetch_Meta` for returning data.frame of object meta data.  
+- Added `Extract_Sample_Meta` to extract sample-level meta data from object.  
+- Added `Cell_Highlight_Plot` for highlight plots of custom cells not in active ident or meta data.  
+- Added `flip` parameter to `Clustered_DotPlot` to enable axes flipping ([#69](https://github.com/samuel-marsh/scCustomize/issues/69)).  
+
+## Changed  
+- Updated Imports/Suggests for CRAN compatibility.  
+- Under the hood code updates for CRAN compatibility.  
+- Rearrange base R code within `R/` scripts for better organization.  
+
+## Fixes  
+- Fixed missing documentation for number of package functions.  
+- Typo/styling fixes.  
+
+
 # scCustomize 1.0.2 (2022-11-22)  
 ## Added  
 - None.