Merge pull request stemangiola#68 from stemangiola/drop-bind-generics

Drop bind generics
Biomiha · Jun 20, 2023 · 4964d34 · 4964d34
2 parents 1cce7e5 + e976f6b
commit 4964d34
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Showing 9 changed files with 66 additions and 81 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,7 +9,7 @@ Description: tidySingleCellExperiment is an adapter that abstracts the 'SingleCe
 License: GPL-3
 Depends:
     R (>= 4.1.0),
-    ttservice,
+    ttservice (>= 0.3.6),
     SingleCellExperiment
 Imports:
     SummarizedExperiment,
@@ -32,7 +32,8 @@ Imports:
     stringr,
     cli,
     fansi,
-    Matrix
+    Matrix,
+    stats
 Suggests:
     BiocStyle,
     testthat,
@@ -47,8 +48,7 @@ Suggests:
     GGally,
     uwot,
     celldex,
-    dittoSeq,
-    EnsDb.Hsapiens.v86
+    dittoSeq
 VignetteBuilder: 
     knitr
 RdMacros:

diff --git a/NAMESPACE b/NAMESPACE
@@ -4,9 +4,7 @@ S3method(add_count,SingleCellExperiment)
 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(distinct,SingleCellExperiment)
 S3method(extract,SingleCellExperiment)
@@ -78,8 +76,6 @@ export(tidy)
 export(unite)
 export(unnest)
 export(unnest_single_cell_experiment)
-import(dplyr)
-import(tidyr)
 importFrom(Matrix,rowSums)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
@@ -92,9 +88,11 @@ importFrom(SummarizedExperiment,colData)
 importFrom(cli,cat_line)
 importFrom(dplyr,add_count)
 importFrom(dplyr,arrange)
+importFrom(dplyr,contains)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,distinct_at)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
@@ -112,6 +110,7 @@ importFrom(dplyr,select)
 importFrom(dplyr,select_if)
 importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
+importFrom(dplyr,vars)
 importFrom(ellipsis,check_dots_unnamed)
 importFrom(ellipsis,check_dots_used)
 importFrom(fansi,strwrap_ctl)
@@ -123,6 +122,7 @@ importFrom(magrittr,"%>%")
 importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(methods,as)
+importFrom(methods,getMethod)
 importFrom(pillar,align)
 importFrom(pillar,get_extent)
 importFrom(pillar,style_subtle)
@@ -149,6 +149,7 @@ importFrom(rlang,quo_is_symbol)
 importFrom(rlang,quo_is_symbolic)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)
@@ -165,6 +166,8 @@ importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(ttservice,aggregate_cells)
+importFrom(ttservice,bind_cols)
+importFrom(ttservice,bind_rows)
 importFrom(ttservice,join_features)
 importFrom(utils,data)
 importFrom(utils,tail)

diff --git a/R/dplyr_methods.R b/R/dplyr_methods.R
@@ -87,7 +87,7 @@ arrange.SingleCellExperiment <- function(.data, ..., .by_group=FALSE) {
 #'
 #'   When column-binding, rows are matched by position, so all data
 #'   frames must have the same number of rows. To match by value, not
-#'   position, see [mutate-joins].
+#'   position, see mutate-joins.
 #' @param .id Data frame identifier.
 #'
 #'   When `.id` is supplied, a new column of identifiers is
@@ -96,36 +96,24 @@ arrange.SingleCellExperiment <- function(.data, ..., .by_group=FALSE) {
 #'   list of data frames is supplied, the labels are taken from the
 #'   names of the list. If no names are found a numeric sequence is
 #'   used instead.
-#' @param add.cell.ids from SingleCellExperiment 3.0 A character vector of
-#'   length(x=c(x, y)). Appends the corresponding values to the start of each
-#'   objects' cell names.
+#' @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
-#' `%>%` <- magrittr::`%>%`
-#' tt <- pbmc_small
-#' bind_rows(tt, tt)
+#' `%>%` = magrittr::`%>%`
+#' tt = pbmc_small
+#' bind_rows(    tt, tt  )
 #'
-#' tt_bind <- tt %>% select(nCount_RNA, nFeature_RNA)
+#' 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
@@ -155,25 +143,21 @@ bind_rows.SingleCellExperiment <- function(..., .id=NULL, add.cell.ids=NULL) {
 bind_cols_ = function(..., .id=NULL) {
     tts <- tts <- flatten_if(dots_values(...), is_spliced)
 
-    colData(tts[[1]]) <- dplyr::bind_cols(colData(tts[[1]]) %>% as.data.frame(),
+    colData(tts[[1]]) <- bind_cols(colData(tts[[1]]) %>% as.data.frame(),
                                           tts[[2]], .id=.id) %>% DataFrame()
 
     tts[[1]]
 }
 
 #' @export
 #'
-#' @inheritParams bind
+#' @importFrom ttservice bind_cols
+#' @inheritParams bind_cols
+#' 
+#' @name 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

diff --git a/R/methods.R b/R/methods.R
@@ -1,4 +1,5 @@
 
+#' @importFrom methods getMethod
 setMethod(
     f = "show",
     signature = "SingleCellExperiment",
@@ -55,6 +56,9 @@ NULL
 
 #' join_features
 #'
+#' @importFrom dplyr contains
+#' @importFrom dplyr everything
+#'
 #' @docType methods
 #' @rdname join_features
 #'
@@ -173,6 +177,9 @@ setMethod("aggregate_cells", "SingleCellExperiment",  function(.data,
                                                     assays = NULL, 
                                                     aggregation_function = Matrix::rowSums){
 
+  # Fix NOTEs
+  feature = NULL
+
   .sample = enquo(.sample)
 
   # Subset only wanted assays
@@ -192,7 +199,7 @@ setMethod("aggregate_cells", "SingleCellExperiment",  function(.data,
 
                           # Get counts
                           ~  .x %>%
-                            aggregation_function(na.rm = T) %>%
+                            aggregation_function(na.rm = TRUE) %>%
                             enframe(
                               name  = "feature",
                               value = sprintf("%s", .y)

diff --git a/R/tibble_methods.R b/R/tibble_methods.R
@@ -82,7 +82,7 @@ as_tibble.SingleCellExperiment <- function(x, ...,
         when(
 
             # Only if I have reduced dimensions and special datasets
-            ncol(x@int_colData@listData$reducedDims) > 0 ~ (.) %>% dplyr::bind_cols(
+            ncol(x@int_colData@listData$reducedDims) > 0 ~ (.) %>% bind_cols(
               special_datasets_to_tibble(x, ...)
             ),
 

diff --git a/R/tidybulk_utilities.R b/R/tidybulk_utilities.R
@@ -3,8 +3,6 @@
 #' @keywords internal
 #' @noRd
 #'
-#' @import dplyr
-#' @import tidyr
 #' @importFrom purrr as_mapper
 #' @importFrom magrittr equals
 #'
@@ -47,6 +45,10 @@ as_SummarizedExperiment = function(.data,
                                     .transcript = NULL,
                                     .abundance = NULL) {
 
+  # Fix NOTES
+  . = NULL
+  assay = NULL
+
   # Get column names
   .sample = enquo(.sample)
   .transcript = enquo(.transcript)
@@ -167,23 +169,27 @@ get_sample_transcript_counts = function(.data, .sample, .transcript, .abundance)
   if( quo_is_symbolic(.sample) ) .sample = .sample
   else if(".sample" %in% (.data %>% get_tt_columns() %>% names))
     .sample =  get_tt_columns(.data)$.sample
-  else my_stop()
+  else stop()
 
   if( quo_is_symbolic(.transcript) ) .transcript = .transcript
   else if(".transcript" %in% (.data %>% get_tt_columns() %>% names))
     .transcript =  get_tt_columns(.data)$.transcript
-  else my_stop()
+  else stop()
 
   if(  quo_is_symbolic(.abundance) ) .abundance = .abundance
   else if(".abundance" %in% (.data %>% get_tt_columns() %>% names))
     .abundance = get_tt_columns(.data)$.abundance
-  else my_stop()
+  else stop()
 
   list(.sample = .sample, .transcript = .transcript, .abundance = .abundance)
 
 }
 
 get_tt_columns = function(.data){
+
+  # Fix NOTES
+  tt_columns = NULL
+
   if(
     .data %>% attr("internals") %>% is.list() &&
     "tt_columns" %in% names(.data %>% attr("internals"))
@@ -313,8 +319,6 @@ get_x_y_annotation_columns = function(.data, .horizontal, .vertical, .abundance,
 #' @keywords internal
 #' @noRd
 #'
-#' @import dplyr
-#' @import tidyr
 #' @importFrom magrittr set_rownames
 #' @importFrom rlang quo_is_null
 #'
@@ -330,6 +334,10 @@ get_x_y_annotation_columns = function(.data, .horizontal, .vertical, .abundance,
 as_matrix <- function(tbl,
                       rownames = NULL,
                       do_check = TRUE) {
+
+  # Fix NOTEs
+  variable = NULL
+
   rownames = enquo(rownames)
   tbl %>%
 

diff --git a/R/utilities.R b/R/utilities.R
@@ -84,6 +84,7 @@ drop_class <- function(var, name) {
 #' @importFrom magrittr "%$%"
 #' @importFrom utils tail
 #' @importFrom SummarizedExperiment assays
+#' @importFrom stats setNames
 #'
 #' @param .data A tidySingleCellExperiment
 #' @param features A character
@@ -434,7 +435,7 @@ special_datasets_to_tibble = function(.singleCellExperiment, ...){
       # Otherwise continue normally
       ~ as_tibble(.)
     )) %>%
-    reduce(dplyr::bind_cols)
+    reduce(bind_cols)
 
   # To avoid name change by the bind_cols of as_tibble
   colnames(x) = colnames(x) |> trick_to_avoid_renaming_of_already_unique_columns_by_dplyr()
@@ -456,6 +457,7 @@ trick_to_avoid_renaming_of_already_unique_columns_by_dplyr = function(x){
 #' @importFrom purrr map
 #' @importFrom dplyr distinct_at
 #' @importFrom magrittr equals
+#' @importFrom dplyr vars
 #' 
 #' @param .data A tibble
 #' @param .col A vector of column names

diff --git a/man/bind.Rd → man/bind_rows.Rd b/man/bind.Rd → man/bind_rows.Rd