Merge pull request #142 from samuel-marsh/release/2.0.1

Release/2.0.1

Author: samuel-marsh

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 2.0.0
-Date: 2023-11-14 01:30:08 UTC
-SHA: 8987da5397b33ac79a5a3a08da9f7eccfac71a03
+Version: 2.0.1
+Date: 2023-11-17 15:28:31 UTC
+SHA: 2bf5f1166ee097878adef4e10d1a3923db44557b

DESCRIPTION

@@ -1,9 +1,9 @@
 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: 2.0.0
-Date: 2023-11-13
+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: 2.0.1
+Date: 2023-11-17
 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"),

NEWS.md

@@ -1,3 +1,20 @@
+# scCustomize 2.0.1 (2023-11-17)  
+## Added  
+- None.   
+
+  
+## Changed  
+- Removed warning in `VariableFeaturePlot_scCustom` now fixed in Seurat release.  
+   
+
+## Fixes  
+- Fixed error in `Add_Mito_Ribo_Seurat` causing failure due to error message when `overwrite = TRUE`.  
+- Fixed error in `Add_Top_Gene_Pct_Seurat` to avoid issue that accidentally could call function on normalized data.  
+- Fixed error in `Add_Top_Gene_Pct_Seurat` that caused error if more than one counts layer was present.
+- Fixed error in `QC_Histogram` that prevented plotting or titling of plots.  
+
+
+
 # scCustomize 2.0.0 (2023-11-13)  
 ## Added  
 - Added support for metrics produced by Cell Ranger `multi` pipeline to `Read10X_Metrics` via new parameter `cellranger_multi`.

R/Internal_Utilities.R

@@ -654,7 +654,7 @@ Retrieve_Ensembl_Ribo <- function(
        )
      }
      cli_inform(message = c("Columns with {.val {oxphos_name}} and/or {.val {apop_name}} already present in meta.data slot.",
-                            "i" = "Overwriting those columns as .code {overwrite = TRUE.}")
+                            "i" = "Overwriting those columns as {.code overwrite = TRUE.}")
      )
    }
 
@@ -739,7 +739,7 @@ Retrieve_Ensembl_Ribo <- function(
        )
      }
      cli_inform(message = c("Column with {.val {ieg_name}} already present in meta.data slot.",
-                            "i" = "Overwriting those column as .code {overwrite = TRUE.}")
+                            "i" = "Overwriting those column as {.code overwrite = TRUE.}")
      )
    }
 

R/Object_Utilities.R

@@ -183,7 +183,7 @@ Add_Mito_Ribo_Seurat <- function(
       )
     }
     cli_inform(message = c("Columns with {.val {mito_name}} and/or {.val {ribo_name}} already present in meta.data slot.",
-                           "i" = "Overwriting those columns as .code {overwrite = TRUE.}")
+                           "i" = "Overwriting those columns as {.code overwrite = TRUE.}")
     )
   }
 
@@ -391,9 +391,10 @@ Add_Cell_Complexity_Seurat <- function(
 #' storing corrected and uncorrected assays in same object (e.g. outputs of both Cell Ranger and Cell Bender).
 #' @param overwrite Logical.  Whether to overwrite existing an meta.data column.  Default is FALSE meaning that
 #' function will abort if column with name provided to `meta_col_name` is present in meta.data slot.
+#' @param verbose logical, whether to print messages with status updates, default is TRUE.
 #'
 #' @import cli
-#' @importFrom dplyr select all_of
+#' @importFrom dplyr select all_of bind_rows
 #' @importFrom magrittr "%>%"
 #' @importFrom rlang is_installed
 #' @importFrom SeuratObject LayerData
@@ -425,7 +426,8 @@ Add_Top_Gene_Pct_Seurat <- function(
     num_top_genes = 50,
     meta_col_name = NULL,
     assay = "RNA",
-    overwrite = FALSE
+    overwrite = FALSE,
+    verbose = TRUE
 ){
   # Check for scuttle first
   scuttle_check <- is_installed(pkg = "scuttle")
@@ -468,15 +470,47 @@ Add_Top_Gene_Pct_Seurat <- function(
     )
   }
 
+  count_layers_present <- Layers(object = seurat_object, search = "counts")
+
   # Extract matrix
-  count_mat <- LayerData(object = seurat_object, assay = assay)
+  if (length(x = count_layers_present) == 1) {
+    if (isTRUE(x = verbose)) {
+      cli_inform(message = "Calculating percent expressing top {num_top_genes} for layer: {.field {count_layers_present}}")
+    }
+
+    count_mat <- LayerData(object = seurat_object, assay = assay, layer = "counts")
+
+    # calculate
+    res <- as.data.frame(scuttle::perCellQCMetrics(x = count_mat, percent.top = num_top_genes))
+
+    # select percent column
+    res <- res %>%
+      select(all_of(scuttle_colname))
+  }
+
+
+  if (length(x = count_layers_present) > 1) {
+    res_list <- lapply(1:length(x = count_layers_present), function(x) {
+      if (isTRUE(x = verbose)) {
+        cli_inform(message = "Calculating percent expressing top {num_top_genes} for layer: {.field {count_layers_present[x]}}")
+      }
 
-  # calculate
-  res <- as.data.frame(scuttle::perCellQCMetrics(x = count_mat, percent.top = num_top_genes))
+      # Get layer data
+      layer_count <- LayerData(object = seurat_object, assay = assay, layer = count_layers_present[x])
 
-  # select percent column
-  res <- res %>%
-    select(all_of(scuttle_colname))
+      # run scuttle
+      layer_res <- as.data.frame(scuttle::perCellQCMetrics(x = layer_count, percent.top = num_top_genes))
+      # select results column
+      layer_res <- layer_res %>%
+        select(all_of(scuttle_colname))
+    })
+
+    # combine results
+    if (isTRUE(x = verbose)) {
+      cli_inform(message = "Combining data from: {.field {count_layers_present}}")
+    }
+    res <- bind_rows(res_list)
+  }
 
   # Add to object and return
   seurat_object <- AddMetaData(object = seurat_object, metadata = res, col.name = meta_col_name)

R/QC_Plotting_Seurat.R

@@ -632,12 +632,14 @@ QC_Histogram <- function(
   }
 
   # Check and set titles
-  if (is.null(x = plot_title) && is.null(x = split.by)) {
-    plot_titles <- all_found_features
+  if (!is.null(x = plot_title) && length(x = plot_title) != length(x = features)) {
+    cli_abort(message = "The number of {.code plot_title} (.field {length(x = plot_title)}}) does not equal number of features ({.field {length(x = all_found_features)}})")
+  } else {
+    plot_titles <- plot_title
   }
 
-  if (!is.null(x = plot_title) && length(x = plot_title) != features) {
-    cli_abort(message = "The number of {.code plot_title} (.field {length(x = plot_title)}}) does not equal number of features ({.field {length(x = all_found_features)}})")
+  if (is.null(x = plot_title) && is.null(x = split.by)) {
+    plot_titles <- all_found_features
   }
 
   # Plot

R/Seurat_Plotting.R

@@ -2582,12 +2582,6 @@ VariableFeaturePlot_scCustom <- function(
   # set assay (if null set to active assay)
   assay <- assay %||% DefaultAssay(object = seurat_object)
 
-  if (isTRUE(x = Assay5_Check(seurat_object = seurat_object, assay = assay))) {
-    cli_inform(message = c("!" = "Currently labeling top variable genes from Assay5 object will not correctly label top variable features due to changes in Seurat5.",
-                                "i" = "This feature will be updated when more information comes from Seurat Dev team.",
-                                "i" = "For now the top variable features can be manually extracted and provided to {.code custom_features} parameter."))
-  }
-
   # Extract num of desired features
   top_features <- head(x = VariableFeatures(object = seurat_object, assay = assay, selection.method = selection.method), num_features)
 

cran-comments.md

@@ -1,9 +1,7 @@
 ## Minor Version Update 
-This is a major version update to v2.0.0. In this version I have:  
+This is a hotfix update with bug fixes now v2.0.1; apologies for not catching these in v2.0.0 submission last week. In this version I have:  
 
-- Added a number of new functions, added new function parameters, and fixed bugs (see News.md).  
-- Ensured compatibility with major version of Seurat package.  
-- Fixed in example code causing current CRAN check errors with current package version (v1.1.3).
+- Fixed 5 minor bugs presented in v2.0.0 release.
 
 
 ## R CMD check results
@@ -29,5 +27,5 @@ This is a major version update to v2.0.0. In this version I have:
     - The errors are from failures running package examples.  This includes functions that have been part of prior CRAN releases.
     NO errors are found when checking locally on macos platform using R 4.3.2 and none are found in GitHub Actions check on linux
     or windows platforms.  I believe to be error in GitHub Actions workflow and I have therefore refrained from adding `dontrun`
-    to examples that run fine on other platforms.  If error occurs during CRAN check during submission I will re-evaluate changes
-    required.  
+    to examples that run fine on other platforms.  This was also the case with v2.0.0 which passed macos checks on CRAN,
+    furthering it is likely a GitHub Actions issue.