Drop bind generics

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: tidyseurat
 Title: Brings Seurat to the Tidyverse 
-Version: 0.6.0
+Version: 0.6.1
 Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]",
                   role = c("aut", "cre")),
             person("Maria", "Doyle", email = "[email protected]",
@@ -34,7 +34,6 @@ Imports:
     stringr,
     cli,
     fansi,
-    pkgconfig,
     Matrix
 Suggests:
     testthat,

NAMESPACE

@@ -4,9 +4,7 @@ S3method(add_count,Seurat)
 S3method(arrange,Seurat)
 S3method(as_tibble,Seurat)
 S3method(bind_cols,Seurat)
-S3method(bind_cols,default)
 S3method(bind_rows,Seurat)
-S3method(bind_rows,default)
 S3method(count,Seurat)
 S3method(distinct,Seurat)
 S3method(extract,Seurat)
@@ -41,11 +39,11 @@ S3method(tidy,Seurat)
 S3method(unite,Seurat)
 S3method(unnest,tidyseurat_nested)
 export("%>%")
+export()
 export(add_count)
 export(aggregate_cells)
 export(arrange)
 export(as_tibble)
-export(bind_cols)
 export(bind_rows)
 export(count)
 export(distinct)
@@ -93,6 +91,7 @@ importFrom(dplyr,arrange)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
@@ -161,6 +160,8 @@ importFrom(tidyr,spread)
 importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
 importFrom(ttservice,aggregate_cells)
+importFrom(ttservice,bind_cols)
+importFrom(ttservice,bind_rows)
 importFrom(ttservice,join_features)
 importFrom(utils,packageDescription)
 importFrom(utils,tail)

R/dplyr_methods.R

@@ -65,7 +65,6 @@ arrange.Seurat <- function(.data, ..., .by_group = FALSE) {
 }
 
 
-
 #' Efficiently bind multiple data frames by row and column
 #'
 #' This is an efficient implementation of the common pattern of
@@ -96,6 +95,8 @@ arrange.Seurat <- function(.data, ..., .by_group = FALSE) {
 #'   used instead.
 #' @param add.cell.ids from Seurat 3.0 A character vector of length(x = c(x, y)). Appends the corresponding values to the start of each objects' cell names.
 #'
+#' @importFrom ttservice bind_rows
+#'
 #' @return `bind_rows()` and `bind_cols()` return the same type as
 #'   the first input, either a data frame, `tbl_df`, or `grouped_df`.
 #' @examples
@@ -106,25 +107,10 @@ arrange.Seurat <- function(.data, ..., .by_group = FALSE) {
 #' tt_bind = tt %>% select(nCount_RNA ,nFeature_RNA)
 #' tt %>% bind_cols(tt_bind)
 #'
-#' @name bind
-NULL
-
-
-#' @rdname dplyr-methods
-#'
-#' @inheritParams bind
-#'
-#' @export
-#'
-bind_rows <- function(..., .id = NULL,  add.cell.ids = NULL) {
-  UseMethod("bind_rows")
-}
-
 #' @export
-bind_rows.default <-  function(..., .id = NULL,  add.cell.ids = NULL)
-{
-  dplyr::bind_rows(..., .id = .id)
-}
+#' 
+#' @name bind_rows
+NULL
 
 #' @importFrom rlang dots_values
 #' @importFrom rlang flatten_if
@@ -154,26 +140,19 @@ bind_cols_ = function(..., .id = NULL){
 
   tts = flatten_if(dots_values(...), is_spliced)
 
-  tts[[1]]@meta.data = dplyr::bind_cols( tts[[1]][[]], tts[[2]], .id = .id)
+  tts[[1]]@meta.data = bind_cols( tts[[1]][[]], tts[[2]], .id = .id)
 
   tts[[1]]
 
 }
 
 #' @export
 #'
-#' @inheritParams bind
+#' @importFrom ttservice bind_cols
+#' @inheritParams bind_cols
 #'
 #' @rdname dplyr-methods
-bind_cols <- function(..., .id = NULL) {
-  UseMethod("bind_cols")
-}
-
-#' @export
-bind_cols.default <-  function(..., .id = NULL)
-{
-  dplyr::bind_cols(..., .id = .id)
-}
+NULL
 
 #' @importFrom rlang dots_values
 #' @importFrom rlang flatten_if
@@ -183,7 +162,6 @@ bind_cols.default <-  function(..., .id = NULL)
 #'
 bind_cols.Seurat <- bind_cols_
 
-
 #' distinct
 #'
 #' @importFrom dplyr distinct

R/methods.R

@@ -166,6 +166,8 @@ NULL
 
 #' aggregate_cells
 #'
+#' @importFrom dplyr everything
+#' 
 #' @docType methods
 #' @rdname aggregate_cells
 #'
@@ -176,6 +178,10 @@ setMethod("aggregate_cells", "Seurat",  function(.data,
                                                  slot = "data",
                                                  assays = NULL, 
                                                  aggregation_function = Matrix::rowSums){
+  # Solve NOTE  
+  data = NULL
+  .feature = NULL
+
 
     .sample = enquo(.sample)
 

R/tibble_methods.R

@@ -67,7 +67,7 @@ NULL
 #'
 as_tibble.Seurat = function(x, ...,
                      .name_repair = c("check_unique", "unique", "universal", "minimal"),
-                     rownames = pkgconfig::get_config("tibble::rownames", NULL)){
+                     rownames = NULL){
   x[[]] %>%
     tibble::as_tibble(rownames=c_(x)$name) %>%