Merge pull request #92 from stemangiola/fix-drop-argument-deprecation-dplyr

Fix drop argument deprecation dplyr

Author: stemangiola

.gitignore

@@ -16,3 +16,4 @@ dev/dplyr-master/*
 tidyseurat.Rproj
 /doc/
 /Meta/
+..Rcheck/*

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyseurat
 Title: Brings Seurat to the Tidyverse 
-Version: 0.8.8
+Version: 0.8.9
 Authors@R: c(person("Stefano", "Mangiola", email = "mangiolastefano@gmail.com",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "Maria.Doyle@petermac.org",

NAMESPACE

@@ -61,7 +61,6 @@ importFrom(Seurat,SplitObject)
 importFrom(Seurat,VariableFeatures)
 importFrom(SeuratObject,"DefaultAssay<-")
 importFrom(SeuratObject,DefaultAssay)
-importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
 importFrom(dplyr,contains)
 importFrom(dplyr,count)
@@ -129,6 +128,7 @@ importFrom(rlang,is_spliced)
 importFrom(rlang,names2)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(rlang,sym)
 importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)

R/dplyr_methods.R

@@ -952,27 +952,36 @@ add_count <- function(x, ..., wt=NULL, sort=FALSE, name=NULL) {
 #' @export
 #' @rdname count
 add_count.default <- function(x, ..., wt=NULL, sort=FALSE, name=NULL) {
-    dplyr::add_count(x=x, ..., wt=!!enquo(wt), sort=sort, name=name)
+    if (is.null(name)) name <- "n"
+    .out <- x %>%
+        dplyr::group_by(..., .add = TRUE) %>%
+        dplyr::mutate(!!rlang::sym(name) := if (is.null(wt)) dplyr::n() else sum(!!enquo(wt), na.rm = TRUE)) %>%
+        dplyr::ungroup()
+    if (sort) .out <- dplyr::arrange(.out, dplyr::desc(!!rlang::sym(name)))
+    .out
 }
 
 #' @rdname count
 #' @aliases add_count
-#' @importFrom dplyr add_count
+#' @importFrom rlang sym
 #' @export
 add_count.Seurat <- function(x, ..., wt=NULL, sort=FALSE, name=NULL) {
 
     # Deprecation of special column names
-    .cols <- enquos(..., .ignore_empty="all") %>% 
+    .cols <- enquos(..., .ignore_empty="all") %>%
         map(~ quo_name(.x)) %>% unlist()
     if (is_sample_feature_deprecated_used(x, .cols)) {
         x <- ping_old_special_column_into_metadata(x)
     }
 
-    x@meta.data <-
-        x %>%
+    if (is.null(name)) name <- "n"
+    .out <- x %>%
         as_tibble %>%
-        dplyr::add_count(..., wt=!!enquo(wt), sort=sort, name=name) %>%
-        as_meta_data(x)
+        dplyr::group_by(..., .add = TRUE) %>%
+        dplyr::mutate(!!sym(name) := if (is.null(wt)) dplyr::n() else sum(!!enquo(wt), na.rm = TRUE)) %>%
+        dplyr::ungroup()
+    if (sort) .out <- dplyr::arrange(.out, dplyr::desc(!!sym(name)))
+    x@meta.data <- .out %>% as_meta_data(x)
 
     x
 }

inst/NEWS.rd

@@ -1,6 +1,11 @@
 \name{NEWS}
 \title{News for Package \pkg{tidyseurat}}
 
+\section{Changes in version 0.8.9}{
+\itemize{
+    \item CRAN fix: \code{add_count()} now uses \code{count(..., .add = TRUE)} instead of \code{dplyr::add_count()}, avoiding the defunct \code{.drop} argument (dplyr 1.0.0+).
+}}
+
 \section{Changes in version 0.8.8}{
 \itemize{
     \item Removed deprecated \code{.drop} argument from \code{add_count.Seurat()} to align with dplyr's API changes