Merge pull request #55 from stemangiola/add_count-drop-generics

Add count drop generics

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidySingleCellExperiment
 Title: Brings SingleCellExperiment to the Tidyverse 
-Version: 1.9.2
+Version: 1.9.3
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")) )
 Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCellExperiment' container 

NAMESPACE

@@ -1,15 +1,13 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(add_count,SingleCellExperiment)
-S3method(add_count,default)
 S3method(arrange,SingleCellExperiment)
 S3method(as_tibble,SingleCellExperiment)
 S3method(bind_cols,SingleCellExperiment)
 S3method(bind_cols,default)
 S3method(bind_rows,SingleCellExperiment)
 S3method(bind_rows,default)
 S3method(count,SingleCellExperiment)
-S3method(count,default)
 S3method(distinct,SingleCellExperiment)
 S3method(extract,SingleCellExperiment)
 S3method(filter,SingleCellExperiment)
@@ -87,6 +85,7 @@ importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(cli,cat_line)
+importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)

R/dplyr_methods.R

@@ -1278,6 +1278,7 @@ sample_frac.SingleCellExperiment <- function(tbl, size=1, replace=FALSE,
 
 #' Count observations by group
 #'
+#' @importFrom dplyr count
 #'
 #' @description
 #' `count()` lets you quickly count the unique values of one or more variables:
@@ -1311,30 +1312,19 @@ sample_frac.SingleCellExperiment <- function(tbl, size=1, replace=FALSE,
 #' An object of the same type as `.data`. `count()` and `add_count()`
 #' group transiently, so the output has the same groups as the input.
 #' @export
+#'
+#' @rdname dplyr-methods
+#' @name count
+#'
 #' @examples
 #'
+#'
 #' `%>%` <- magrittr::`%>%`
 #' pbmc_small %>%
 #'
 #'     count(groups)
-count <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
-    UseMethod("count")
-}
+NULL
 
-#' @export
-count.default <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
-    if (!missing(...)) {
-        out <- dplyr::group_by(x, ..., .add=TRUE, .drop=.drop)
-    }
-    else {
-        out <- x
-    }
-    out <- dplyr::tally(out, wt=!!enquo(wt), sort=sort, name=name)
-    if (is.data.frame(x)) {
-        out <- dplyr::dplyr_reconstruct(out, x)
-    }
-    out
-}
 #' @export
 count.SingleCellExperiment <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .drop=group_by_drop_default(x)) {
     message(data_frame_returned_message)
@@ -1352,23 +1342,19 @@ count.SingleCellExperiment <- function(x, ..., wt=NULL, sort=FALSE, name=NULL, .
         dplyr::count(..., wt=!!enquo(wt), sort=sort, name=name, .drop=.drop)
 }
 
-#' @export
-#' @rdname count
-add_count <- function(x, ..., wt = NULL, sort = FALSE, name = NULL, .drop = group_by_drop_default(x)) {
-    UseMethod("add_count")
-}
 
 #' @export
-#' @rdname count
-add_count.default <- function(x, ..., wt = NULL, sort = FALSE, name = NULL, .drop = group_by_drop_default(x)) {
-
-    dplyr::add_count(x=x, ..., wt = !!enquo(wt), sort = sort, name = name, .drop = .drop)
-
-}
+#'
+#'
+#' @importFrom dplyr add_count
+#'
+#' @name add_count
+#'
+#' @rdname dplyr-methods
+NULL
 
 #' @export
-#' @rdname count
-add_count.SingleCellExperiment <- function(x, ..., wt = NULL, sort = FALSE, name = NULL, .drop = group_by_drop_default(x)) {
+add_count.SingleCellExperiment <- function(x, ..., wt = NULL, sort = FALSE, name = NULL) {
 
   # Deprecation of special column names
   if(is_sample_feature_deprecated_used(
@@ -1378,16 +1364,18 @@ add_count.SingleCellExperiment <- function(x, ..., wt = NULL, sort = FALSE, name
     x= ping_old_special_column_into_metadata(x)
   }
 
-    colData(x) =
-        x %>%
-        as_tibble %>%
-        dplyr::add_count(..., wt = !!enquo(wt), sort = sort, name = name, .drop = .drop)  %>%
-        as_meta_data(x)
+  colData(x) =
+    x %>%
+    as_tibble %>%
+    dplyr::add_count(..., wt = !!enquo(wt), sort = sort, name = name)  %>%
+    as_meta_data(x)
 
-    x
+  x
 
 }
 
+
+
 #' Extract a single column
 #'
 #'

tests/testthat/test-dplyr_methods.R

@@ -172,3 +172,10 @@ test_that("count", {
         nrow() %>%
         expect_equal(2)
 })
+
+test_that("add count", {
+  pbmc_small %>%
+    add_count(groups) %>%
+    nrow() %>%
+    expect_equal(230)
+})