Merge pull request #86 from samuel-marsh/release/1.1.1

Release 1.1.1 release

Author: samuel-marsh

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.1.0
-Date: 2022-12-22 21:24:58 UTC
-SHA: f0aff7dee2b0af306b2a055748640c8b31ccdebc
+Version: 1.1.1
+Date: 2023-01-13 15:02:59 UTC
+SHA: a78523f9f8648a034a64a2f7455ddb8acfbca410

DESCRIPTION

@@ -2,15 +2,15 @@ Package: scCustomize
 Type: Package
 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
+Version: 1.1.1
+Date: 2023-01-13
 Authors@R: c(
     person(given = "Samuel", family = "Marsh", email = "samuel.marsh@childrens.harvard.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3012-6945")),
     person(given = "Ming", family = "Tang", role = c("ctb"), email = "tangming2005@gmail.com"),
     person(given = 'Velina', family = 'Kozareva', role = c('ctb')),
     person("Lucas", "Graybuck", email = "lucasg@alleninstitute.org", role = c('ctb'))
     )
-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
+URL: 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)
@@ -46,8 +46,7 @@ Imports:
     stringi,
     stringr,
     tibble,
-    tidyr,
-    viridis
+    tidyr
 Suggests:
     ComplexHeatmap,
     dittoSeq,
@@ -61,7 +60,8 @@ Suggests:
     rmarkdown,
     tidyselect,
     tidyverse, 
-    qs
+    qs,
+    viridis
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(Fetch_Meta,Seurat)
+S3method(Fetch_Meta,liger)
 export(Add_CellBender_Diff)
 export(Add_Cell_Complexity_LIGER)
 export(Add_Cell_Complexity_Seurat)
@@ -136,7 +138,6 @@ import(parallel)
 import(patchwork)
 import(pbapply)
 import(rlang)
-import(viridis)
 importFrom(Matrix,readMM)
 importFrom(Matrix,rowSums)
 importFrom(Seurat,AddMetaData)
@@ -196,6 +197,7 @@ importFrom(magrittr,"%>%")
 importFrom(methods,as)
 importFrom(methods,new)
 importFrom(methods,slot)
+importFrom(paletteer,paletteer_c)
 importFrom(paletteer,paletteer_d)
 importFrom(patchwork,plot_annotation)
 importFrom(patchwork,plot_layout)

NEWS.md

@@ -1,3 +1,26 @@
+# scCustomize 1.1.1 (2023-01-13)  
+## Added  
+- Added `label_color_num` parameter to `PalettePlot` allow control of color labeling.  
+- Added ability to rotate x-axis of `Stacked_VlnPlot` 90 degrees or 45 (previously possible) ([#84](https://github.com/samuel-marsh/scCustomize/issues/84)).  
+- Added error checks to `Merge_Seurat_List` to avoid ambiguous error messages on failure.  
+- Added `Case_Check` checks/messages to all feature-based plotting functions.  
+  
+## Changed  
+- **BREAKING CHANGE** Parameter in `PalettePlot` has been changed from `palette` to `pal`.  
+- Updated `PalettePlot` to support `pal` of class "colors".  
+- Moved viridis package to Suggests and use paletteer package for viridis palette shortcut functions.  
+- Fixed color palette continuity in `Cluster_Highlight_Plot` and `Meta_Highlight_Plot`.  
+- `Fetch_Meta` is now S3 generic function that can handle either Seurat or LIGER objects.  
+- Rearrange base R code within `R/` scripts for better organization.  
+- Completed move of all scCustomize error/warning messages from base R to cli/rlang framework.  
+- Move feature checking to internal function.  
+
+## Fixes  
+- Fixed potential for column name collision error in `Add_Mito_Ribo_Seurat` and `Add_Mito_Ribo_LIGER`.  
+- Fixed `Add_Mito_Ribo_Seurat` to respect provided `mito_name`, `ribo_name` and `mito_ribo_name` values.  
+- Updated out-dated documentation for number of package functions.  
+- Typo/styling fixes.  
+ 
 # 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`.  
@@ -121,7 +144,7 @@
 
 # scCustomize 0.6.3 (2021-12-16)  
 ## Fixes
-- Fixed `Read_Metrics_10X` errors that occured due to differing outputs depending on Cell Ranger version or type of assay.
+- Fixed `Read_Metrics_10X` errors that occurred due to differing outputs depending on Cell Ranger version or type of assay.
 - Added direct `importFrom` for `DefaultDimReduc` from SeuratObject to avoid potential errors.