Release v3.3.0

DESCRIPTION

@@ -2,14 +2,14 @@ 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> RRID:SCR_024675.
-Version: 3.2.4
-Date: 2025-12-10
+Version: 3.2.4.9012
+Date: 2026-04-02
 Authors@R: c(
     person(given = "Samuel", family = "Marsh", email = "sccustomize@gmail.com", 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')),
-    person("Zoe", "Clarke", email = "zoe.clarke@utoronto.ca", role = c('ctb'), comment = c(ORCID = "0000-0003-0336-8049"))
+    person(given ="Lucas", family = "Graybuck", email = "lucasg@alleninstitute.org", role = c('ctb')),
+    person(given ="Zoe", family = "Clarke", email = "zoe.clarke@utoronto.ca", role = c('ctb'), comment = c(ORCID = "0000-0003-0336-8049"))
     )
 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

NAMESPACE

@@ -144,6 +144,7 @@ export(Read_CellBender_h5_Multi_File)
 export(Read_GEO_Delim)
 export(Read_Metrics_10X)
 export(Read_Metrics_CellBender)
+export(Read_Velocity)
 export(Reduction_Loading_Present)
 export(Rename_Clusters)
 export(Replace_Suffix)

NEWS.md

@@ -1,3 +1,28 @@
+# scCustomize 3.3.0 (2026-XX-XX)  
+## Added  
+- Added `reorder`, `reorder_decreasing`, and `plot_median` parameters to `Plot_Cells_per_Sample` when grouping by sample.  
+- Added `Read_Velocity` function to enable reading of velocyto loom output files without needing to install velocyto.R (which currently suffers from significant installation issues unrelated to reading loom files).  
+
+
+
+## Changed  
+- **BREAKING CHANGE** The `plot_by` parameter has been soft-deprecated in `Seq_QC_Plot_*` family of functions.  Please use `group.by` instead.  Using `plot_by` will warn user but still work until scCustomize v3.5.0.  
+- **BREAKING CHANGE** The parameter `cutoff_line_width` has been soft-deprecated in `QC_Plot_*` family of functions.  Please use `cutoff_linewidth` instead.  Using `cutoff_line_width` will warn user but still work until scCustomize v3.5.0.  
+- **BREAKING CHANGE** The parameter `linewidth` has been soft-deprecated in `ElbowPlot_scCustom` function.  Please use `cutoff_linewidth` instead.  Using `linewidth` will warn user but still work until scCustomize v3.5.0.  
+- Add some checks for appropriate `...` usage.  
+
+
+## Fixes  
+- Fixed default setting of `linewidth` parameter in `geom_hline` and `geom_vline` calls to avoid unnecessary empty aesthetic warnings in ggplot2 4.0.0+.  
+- Fixed warning in `Dataset_Size_LIGER` due to deprecation in `Extract_Sample_Meta`.  
+- Fixed issue with group colors in in `DimPlot_scCustom` when split only contains one group Thanks @zrlewis, ([#262](https://github.com/samuel-marsh/scCustomize/issues/262)).  
+
+
+
+
+
+
+
 # scCustomize 3.2.4 (2025-12-10)  
 ## Added  
 - Add progress bar support to following functions with `parallel` parameter using mcprogress package: `Read10X_GEO`, `Read10X_h5_GEO`, `Read10X_Multi_Directory`, `Read10X_h5_Multi_Directory`, `Read_GEO_Delim`, `Read_CellBender_h5_Multi_Directory`, `Read_CellBender_h5_Multi_File`.  

R/Internal_Utilities.R

@@ -590,7 +590,7 @@ Percent_Expressing_Meta <- function(
   row_dim_names <- features_list
   col_dim_names <- names(x = percent_expressing)
   mat_dims <- list(row_dim_names, col_dim_names)
-  final_df <- data.frame(matrix(unlist(percent_expressing), nrow = length(features_list), byrow = FALSE, dimnames = mat_dims), stringsAsFactors = FALSE)
+  final_df <- data.frame(matrix(unlist(x = percent_expressing), nrow = length(features_list), byrow = FALSE, dimnames = mat_dims), stringsAsFactors = FALSE)
   return(final_df)
 }
 
@@ -645,7 +645,7 @@ Middle_Number <- function(
   max
 ) {
   min_max <- c(min, max)
-  middle <- min_max[-length(min_max)] + diff(min_max) / 2
+  middle <- min_max[-length(x = min_max)] + diff(x = min_max) / 2
   return(middle)
 }
 

R/LIGER_Utilities.R

@@ -581,7 +581,7 @@ Dataset_Size_LIGER <- function(
 
     found_meta <- Meta_Present(object = liger_object, meta_col_names = meta_data_column, print_msg = FALSE)[[1]]
 
-    sample_meta <- Extract_Sample_Meta(object = liger_object, sample_name = "dataset", variables_include = found_meta)
+    sample_meta <- Extract_Sample_Meta(object = liger_object, sample_col = "dataset", variables_include = found_meta)
 
     # join data
     dataset_cells_df <- right_join(x = dataset_cells_df, y = sample_meta, by = join_by("dataset"))
@@ -1096,7 +1096,6 @@ Add_Cell_QC_Metrics.liger <- function(
     add_IEG = TRUE,
     add_hemo = TRUE,
     add_lncRNA = TRUE,
-    add_cell_cycle = TRUE,
     species,
     mito_name = "percent_mito",
     ribo_name = "percent_ribo",