Merge pull request #14 from samuel-marsh/develop

Merge for Version 0.6.3 Release

Author: samuel-marsh

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: scCustomize
 Type: Package
 Title: An R package for custom visualization & analyses of single cell sequencing.
-Version: 0.6.2
-Date: 2021-12-01
+Version: 0.6.3
+Date: 2021-12-16
 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"),

NAMESPACE

@@ -130,6 +130,7 @@ importFrom(Seurat,Read10X_h5)
 importFrom(Seurat,VariableFeaturePlot)
 importFrom(Seurat,VizDimLoadings)
 importFrom(Seurat,VlnPlot)
+importFrom(SeuratObject,DefaultDimReduc)
 importFrom(colorway,varibow)
 importFrom(cowplot,theme_cowplot)
 importFrom(data.table,fread)

NEWS.md

@@ -1,3 +1,9 @@
+# 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.
+- Added direct `importFrom` for `DefaultDimReduc` from SeuratObject to avoid potential errors.
+ 
+
 # scCustomize 0.6.2 (2021-12-01)  
 ## Fixes
 - Fixed barcode name duplication checks in `Merge_Sparse_Data_All`. ([#8](https://github.com/samuel-marsh/scCustomize/issues/8))

R/Other_Package_Plotting.R

@@ -17,6 +17,7 @@
 #'
 #' @import ggplot2
 # #' @importFrom Nebulosa plot_density
+#' @importFrom SeuratObject DefaultDimReduc
 #'
 #' @export
 #'
@@ -100,6 +101,7 @@ Plot_Density_Custom <- function(
 #'
 #' @import ggplot2
 # #' @importFrom Nebulosa plot_density
+#' @importFrom SeuratObject DefaultDimReduc
 #'
 #' @export
 #'

R/Read_&_Write_Data.R

@@ -1098,7 +1098,8 @@ Read_Metrics_10X <- function(
 
     raw_data <- read.csv(file = paste0(file_path, "metrics_summary.csv"), stringsAsFactors = F)
     # Change format of numeric columns to due commas in data csv output.
-    raw_data[,c(1:4, 18:19)] <- lapply(raw_data[,c(1:4, 18:19)],function(x){as.numeric(gsub(",", "", x))})
+    column_numbers <- grep(pattern = ",", x = raw_data[1, ])
+    raw_data[,c(column_numbers)] <- lapply(raw_data[,c(column_numbers)],function(x){as.numeric(gsub(",", "", x))})
     return(raw_data)
   })
 

R/Seurat_Iterative_Plotting.R

@@ -116,6 +116,7 @@ Iterate_PC_Loading_Plots <- function(
 #' @import ggplot2
 #' @importFrom pbapply pblapply pboptions
 #' @importFrom Seurat DimPlot
+#' @importFrom SeuratObject DefaultDimReduc
 #' @importFrom stringr str_detect
 #' @importFrom utils txtProgressBar setTxtProgressBar
 #'
@@ -272,6 +273,7 @@ Iterate_DimPlot_bySample <- function(
 #' @import ggplot2
 #' @importFrom pbapply pbmapply pboptions
 #' @importFrom Seurat DimPlot
+#' @importFrom SeuratObject DefaultDimReduc
 #' @importFrom stringr str_detect
 #' @importFrom utils txtProgressBar setTxtProgressBar
 #'
@@ -466,6 +468,7 @@ Iterate_Cluster_Highlight_Plot <- function(
 #' @importFrom forcats fct_relevel
 #' @importFrom pbapply pbmapply pboptions
 #' @importFrom Seurat DimPlot
+#' @importFrom SeuratObject DefaultDimReduc
 #' @importFrom stringr str_detect
 #' @importFrom utils txtProgressBar setTxtProgressBar
 #'
@@ -692,6 +695,7 @@ Iterate_Meta_Highlight_Plot <- function(
 #' @import ggplot2
 #' @importFrom pbapply pblapply pboptions
 #' @importFrom Seurat FeaturePlot
+#' @importFrom SeuratObject DefaultDimReduc
 #' @importFrom stringr str_detect
 #' @importFrom utils txtProgressBar setTxtProgressBar
 #'
@@ -1067,6 +1071,7 @@ Iterate_VlnPlot <- function(
 #'
 #' @import ggplot2
 #' @importFrom pbapply pblapply pboptions
+#' @importFrom SeuratObject DefaultDimReduc
 #' @importFrom stringr str_detect
 #' @importFrom utils txtProgressBar setTxtProgressBar
 #'
@@ -1258,6 +1263,7 @@ Iterate_Plot_Density_Custom <- function(
 #' @import ggplot2
 #' @importFrom pbapply pblapply pboptions
 #' @importFrom purrr discard keep
+#' @importFrom SeuratObject DefaultDimReduc
 #' @importFrom stringr str_detect
 #' @importFrom utils txtProgressBar setTxtProgressBar
 #'

R/Seurat_Plotting.R

@@ -24,6 +24,7 @@
 #' @import ggplot2
 #' @import patchwork
 #' @importFrom Seurat FeaturePlot
+#' @importFrom SeuratObject DefaultDimReduc
 #'
 #' @export
 #'
@@ -860,6 +861,7 @@ DotPlot_scCustom <- function(
 #'
 #' @import patchwork
 #' @importFrom Seurat DimPlot
+#' @importFrom SeuratObject DefaultDimReduc
 #'
 #' @export
 #'
@@ -1020,6 +1022,7 @@ DimPlot_scCustom <- function(
 #'
 #' @import patchwork
 #' @importFrom Seurat DimPlot
+#' @importFrom SeuratObject DefaultDimReduc
 #'
 #' @export
 #'

README.md

@@ -3,7 +3,6 @@
 
 [![GitHub release (latest by
 date)](https://img.shields.io/github/v/release/samuel-marsh/scCustomize?color=gree)](https://github.com/samuel-marsh/scCustomize/releases)
-[![R-CMD-check](https://github.com/samuel-marsh/scCustomize/workflows/R-CMD-check/badge.svg)](https://github.com/samuel-marsh/scCustomize/actions)
 [![license](https://img.shields.io/github/license/samuel-marsh/scCustomize)](https://github.com/samuel-marsh/scCustomize/blob/master/LICENSE)
 [![issues](https://img.shields.io/github/issues/samuel-marsh/scCustomize)](https://github.com/samuel-marsh/scCustomize/issues)
 [![DOI](https://zenodo.org/badge/411807769.svg)](https://zenodo.org/badge/latestdoi/411807769)

index.md

@@ -9,7 +9,6 @@ p.caption {
 
 [![GitHub release (latest by
 date)](https://img.shields.io/github/v/release/samuel-marsh/scCustomize?color=gree)](https://github.com/samuel-marsh/scCustomize/releases)
-[![R-CMD-check](https://github.com/samuel-marsh/scCustomize/workflows/R-CMD-check/badge.svg)](https://github.com/samuel-marsh/scCustomize/actions)
 [![license](https://img.shields.io/github/license/samuel-marsh/scCustomize)](https://github.com/samuel-marsh/scCustomize/blob/master/LICENSE)
 [![issues](https://img.shields.io/github/issues/samuel-marsh/scCustomize)](https://github.com/samuel-marsh/scCustomize/issues)
 [![DOI](https://zenodo.org/badge/411807769.svg)](https://zenodo.org/badge/latestdoi/411807769)