Merge pull request #73 from samuel-marsh/develop

Merge for 1.0.1 Release

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: scCustomize
 Type: Package
 Title: An R package for custom visualization & analyses of single cell sequencing.
-Version: 1.0.0
-Date: 2022-10-25
+Version: 1.0.1
+Date: 2022-11-10
 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]"),
@@ -13,7 +13,7 @@ Description: Collection of functions created and/or curated to aid in the visual
 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 (>= 4.2.0)
+         Seurat (>= 4.2.1)
 Imports: 
     circlize,
     cli (>= 3.2.0),

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(Add_Cell_Bender_Diff)
+export(Add_CellBender_Diff)
 export(Add_Cell_Complexity_LIGER)
 export(Add_Cell_Complexity_Seurat)
 export(Add_Mito_Ribo_LIGER)
@@ -9,6 +9,8 @@ export(Add_Pct_Diff)
 export(Add_Sample_Meta)
 export(Blank_Theme)
 export(Case_Check)
+export(CellBender_Diff_Plot)
+export(CellBender_Feature_Diff)
 export(Change_Delim_All)
 export(Change_Delim_Prefix)
 export(Change_Delim_Suffix)
@@ -131,6 +133,7 @@ import(patchwork)
 import(pbapply)
 import(viridis)
 importFrom(Matrix,readMM)
+importFrom(Matrix,rowSums)
 importFrom(Seurat,AddMetaData)
 importFrom(Seurat,DimPlot)
 importFrom(Seurat,DotPlot)
@@ -150,6 +153,7 @@ importFrom(cowplot,theme_cowplot)
 importFrom(data.table,fread)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
+importFrom(dplyr,desc)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,intersect)
@@ -188,6 +192,7 @@ importFrom(purrr,keep)
 importFrom(purrr,map)
 importFrom(purrr,map2)
 importFrom(purrr,map_dbl)
+importFrom(purrr,pluck)
 importFrom(purrr,reduce)
 importFrom(scales,alpha)
 importFrom(scales,hue_pal)
@@ -203,6 +208,7 @@ importFrom(stringr,str_wrap)
 importFrom(tibble,column_to_rownames)
 importFrom(tibble,rownames_to_column)
 importFrom(tibble,tribble)
+importFrom(tidyr,drop_na)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyselect,all_of)
 importFrom(utils,combn)

NEWS.md

@@ -1,3 +1,16 @@
+# scCustomize 1.0.1 (2022-11-10)  
+## Added  
+- Added `CellBender_Feature_Diff` to return data.frame with count sums and differences between raw and CellBender assays.  
+- Added `CellBender_Diff_Plot` to plot differences between raw and CellBender assays using data from `CellBender_Feature_Diff`.  
+
+## Changed  
+- **BREAKING CHANGE** Function name changed, `Add_CellBender_Diff` is new name for `Add_Cell_Bender_Diff` in order to unify function names for CellBender related functions.  
+- Updated CellBender vignette with new functions.
+
+## Fixes  
+- Fixed for automatic color palette selection when only plotting one group.
+
+
 # scCustomize 1.0.0 (2022-10-25)  
 ## Added
 - Added `mito_name` parameter to `QC_Plots_Mito` to allow for custom specification of meta data column name that contains mitochondrial information.

R/Color_Palettes.R

@@ -522,6 +522,9 @@ scCustomize_Palette <- function(
   if (ggplot_default_colors) {
     colors_use <- Hue_Pal(num_colors = num_groups)
   } else {
+    if (num_groups == 1) {
+      colors_use <- "dodgerblue"
+    }
     if (num_groups == 2) {
       colors_use <- NavyAndOrange()
     }

R/Internal_Utilities.R

@@ -453,3 +453,28 @@ No_Right <- function() {
   )
   return(no.right)
 }
+
+
+#' Symetrical setdiff
+#'
+#' tests for differences between two vectors symmetrically.
+#'
+#' @param x first vector to test
+#' @param y second vector to test
+#'
+#' @return vector differences x vs. y and y vs. x
+#'
+#' @references Function name and code from R-bloggers post:
+#' (https://www.r-bloggers.com/2013/06/symmetric-set-differences-in-r/)
+#'
+#' @keywords internal
+#'
+#' @noRd
+#'
+
+symdiff <- function(
+  x,
+  y
+) {
+  setdiff(x = union(x = x, y = y), intersect(x = x, y = y))
+}

R/Object_Utilities.R

@@ -517,11 +517,11 @@ Add_Sample_Meta <- function(
 #'
 #' @examples
 #' \dontrun{
-#' object <- Add_Cell_Bender_Diff(seurat_object = obj, raw_assay_name = "RAW", cell_bender_assay_name = "RNA")
+#' object <- Add_CellBender_Diff(seurat_object = obj, raw_assay_name = "RAW", cell_bender_assay_name = "RNA")
 #' }
 #'
 
-Add_Cell_Bender_Diff <- function(
+Add_CellBender_Diff <- function(
   seurat_object,
   raw_assay_name,
   cell_bender_assay_name

R/Seurat_Plotting.R

@@ -92,7 +92,7 @@ FeaturePlot_scCustom <- function(
     if (length(x = all_found_features) < 1) {
       cli_abort(message = c("No features were found.",
                             "*" = "The following are not present in object:",
-                            "i" = "{scCustomize:::glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
+                            "i" = "{glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
       )
     }
 
@@ -1011,7 +1011,7 @@ Stacked_VlnPlot <- function(
   if (length(x = all_found_features) < 1) {
     cli_abort(message = c("No features were found.",
                           "*" = "The following are not present in object:",
-                          "i" = "{scCustomize:::glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
+                          "i" = "{glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
     )
   }
 
@@ -1152,7 +1152,7 @@ DotPlot_scCustom <- function(
   if (length(x = all_found_features) < 1) {
     cli_abort(message = c("No features were found.",
                                "*" = "The following are not present in object:",
-                               "i" = "{scCustomize:::glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
+                               "i" = "{glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
     )
   }
 
@@ -1161,7 +1161,7 @@ DotPlot_scCustom <- function(
     op <- options(warn = 1)
     on.exit(options(op))
     cli_warn(message = c("The following features were omitted as they were not found:",
-                              "i" = "{scCustomize:::glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
+                              "i" = "{glue_collapse_scCustom(input_string = all_not_found_features, and = TRUE)}")
     )
   }
 

R/Statistics.R

@@ -279,3 +279,87 @@ Median_Stats <- function(
 }
 
 
+#' CellBender Feature Differences
+#'
+#' Get quick values for raw counts, CellBender counts, count differences, and percent count differences
+#' per feature.
+#'
+#' @param seurat_object Seurat object name.
+#' @param raw_assay Name of the assay containing the raw count data.
+#' @param cell_bender_assay Name of the assay containing the CellBender count data.
+#'
+#' @return A data frame containing summed raw counts, CellBender counts, count difference, and
+#' percent difference in counts.
+#'
+#' @import cli
+#' @importFrom dplyr arrange desc left_join mutate
+#' @importFrom magrittr "%>%"
+#' @importFrom Matrix rowSums
+#' @importFrom purrr pluck
+#' @importFrom tibble rownames_to_column column_to_rownames
+#'
+#' @export
+#'
+#' @concept stats
+#'
+#' @examples
+#' \dontrun{
+#' cb_stats <- CellBender_Feature_Diff(seurat_object - obj, raw_assay = "RAW",
+#' cell_bender_assay = "RNA")
+#' }
+#'
+
+CellBender_Feature_Diff <- function(
+  seurat_object,
+  raw_assay,
+  cell_bender_assay
+) {
+  # Is Seurat
+  Is_Seurat(seurat_object = seurat_object)
+
+  # Check assays present
+  assays_not_found <- Assay_Present(seurat_object = seurat_object, assay_list = c(raw_assay, cell_bender_assay), print_msg = FALSE, omit_warn = TRUE)[[2]]
+
+  if (!is.null(x = assays_not_found)) {
+    stop_quietly()
+  }
+
+  # Pull raw counts
+  raw_counts <- pluck(seurat_object, "assays", raw_assay, "counts") %>%
+    rowSums() %>%
+    data.frame() %>%
+    rownames_to_column("Feature_Names")
+
+  colnames(raw_counts)[2] <- "Raw_Counts"
+
+  # Pull Cell Bender Counts
+  cb_counts <- pluck(seurat_object, "assays", cell_bender_assay, "counts") %>%
+    rowSums() %>%
+    data.frame() %>%
+    rownames_to_column("Feature_Names")
+
+  colnames(cb_counts)[2] <- "CellBender_Counts"
+
+  # Check features identical
+  diff_features <- symdiff(x = raw_counts$Feature_Names, y = cb_counts$Feature_Names)
+
+  if (length(x = diff_features > 0)) {
+    cli_warn(message = c("The following features are not present in both assays:",
+                         "*" = "{diff_features}",
+                         "i" = "Check matrices used to create object.")
+             )
+  }
+
+  # merge
+  merged_counts <- suppressMessages(left_join(x = raw_counts, y = cb_counts))
+
+  # Add diff and % diff
+  merged_counts <- merged_counts %>%
+    mutate(Count_Diff = Raw_Counts - CellBender_Counts,
+           Pct_Diff = 100 - ((CellBender_Counts / Raw_Counts) * 100)) %>%
+    arrange(desc(Pct_Diff)) %>%
+    column_to_rownames("Feature_Names")
+
+  # return data
+  return(merged_counts)
+}