Update documentation

NAMESPACE

@@ -36,8 +36,6 @@ export(rowwise)
 export(slice)
 export(summarise)
 export(unnest_single_cell_experiment)
-import(dplyr)
-import(tidyr)
 importFrom(BiocGenerics,cbind)
 importFrom(BiocGenerics,rbind)
 importFrom(Matrix,rowSums)
@@ -94,6 +92,7 @@ importFrom(rlang,quo_is_symbol)
 importFrom(rlang,quo_is_symbolic)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(rlang,sym)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace_all)
@@ -105,6 +104,7 @@ importFrom(tidyr,nest)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,separate)
 importFrom(tidyr,spread)
+importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(ttservice,bind_cols)

R/dplyr_methods.R

@@ -40,10 +40,7 @@ bind_cols_ = function(..., .id=NULL) {
 #' @examples 
 #' example(read10xVisium)
 #' spe |>
-#'     bind_cols(
-#'         spe |> 
-#'             select(array_row)
-#'     )
+#'    bind_cols(1:99)
 #' 
 #' @export
 bind_cols.SpatialExperiment <- bind_cols_
@@ -452,20 +449,6 @@ NULL
 #'   arrange(array_row)
 NULL
 
-#' @name bind_rows
-#' @rdname bind_rows
-#' @inherit ttservice::bind_rows
-#' 
-#' @examples
-#' example(read10xVisium)
-#' spe |>
-#'    bind_rows(spe)
-#' spe |>
-#'    bind_cols(1:99)
-#'    
-#' @name bind
-NULL
-
 #' @name rename
 #' @rdname rename
 #' @inherit dplyr::rename

R/methods.R

@@ -162,7 +162,7 @@ aggregate_cells <- function(.data, .sample = NULL, slot = "data", assays = NULL,
 
                           # Get counts
                           ~  .x %>%
-                            aggregation_function(na.rm = T) %>%
+                            aggregation_function(na.rm = TRUE) %>%
                             enframe(
                               name  = "feature",
                               value = sprintf("%s", .y)

R/tibble_methods.R

@@ -39,7 +39,7 @@ as_tibble.SpatialExperiment <- 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 ~ (.) %>% cbind(
               special_datasets_to_tibble(x, ...)
             ),
 

R/tidybulk_utilities.R

@@ -3,10 +3,7 @@
 #' @keywords internal
 #' @noRd
 #'
-#' @import dplyr
-#' @import tidyr
 #' @importFrom purrr as_mapper
-#' @importFrom magrittr equals
 #'
 #' @param .x A tibble
 #' @param .p A boolean
@@ -79,8 +76,6 @@ get_x_y_annotation_columns <- tidySingleCellExperiment:::get_x_y_annotation_colu
 #' @keywords internal
 #' @noRd
 #'
-#' @import dplyr
-#' @import tidyr
 #' @importFrom magrittr set_rownames
 #' @importFrom rlang quo_is_null
 #'

R/tidyr_methods.R

@@ -66,6 +66,7 @@ unnest_single_cell_experiment  <-  function(data, cols, ..., keep_empty=FALSE, p
 #' @importFrom tidyr nest
 #' @importFrom rlang enquos
 #' @importFrom rlang :=
+#' @importFrom rlang sym
 #' @export
 nest.SpatialExperiment <- function(.data, ..., .names_sep = NULL) {
     cols <- enquos(...)
@@ -139,6 +140,7 @@ extract.SpatialExperiment <- function(data, col, into, regex="([[:alnum:]]+)", r
 #' spe |>
 #'     unite("A", array_row:array_col)
 #' 
+#' @importFrom tidyr unite
 #' @importFrom SummarizedExperiment colData
 #' @importFrom SummarizedExperiment colData<-
 #' @export