update remaining documentations

cleaning R CMD CHECK

Author: noriakis

DESCRIPTION

@@ -38,7 +38,8 @@ Imports:
     stringr,
     cli,
     fansi,
-    stats
+    stats,
+    pkgconfig
 Suggests:
     BiocStyle,
     testthat,

NAMESPACE

@@ -37,16 +37,8 @@ S3method(tidy,SummarizedExperiment)
 S3method(unite,SummarizedExperiment)
 S3method(unnest,tidySummarizedExperiment_nested)
 export("%>%")
-export(as_tibble)
-export(extract)
-export(nest)
-export(pivot_longer)
-export(pivot_wider)
 export(plot_ly)
-export(separate)
 export(tidy)
-export(unite)
-export(unnest)
 export(unnest_summarized_experiment)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
@@ -55,10 +47,14 @@ importFrom(S4Vectors,head)
 importFrom(S4Vectors,metadata)
 importFrom(SummarizedExperiment,"assays<-")
 importFrom(SummarizedExperiment,"colData<-")
+importFrom(SummarizedExperiment,"elementMetadata<-")
 importFrom(SummarizedExperiment,"rowData<-")
+importFrom(SummarizedExperiment,assay)
+importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,cbind)
 importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,elementMetadata)
 importFrom(SummarizedExperiment,rbind)
 importFrom(SummarizedExperiment,rowData)
 importFrom(SummarizedExperiment,rowRanges)
@@ -85,7 +81,6 @@ importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
 importFrom(dplyr,vars)
-importFrom(ellipsis,check_dots_unnamed)
 importFrom(ellipsis,check_dots_used)
 importFrom(fansi,strwrap_ctl)
 importFrom(ggplot2,aes)
@@ -97,11 +92,13 @@ importFrom(magrittr,equals)
 importFrom(magrittr,set_rownames)
 importFrom(methods,.hasSlot)
 importFrom(methods,as)
+importFrom(methods,getMethod)
 importFrom(methods,is)
 importFrom(pillar,align)
 importFrom(pillar,get_extent)
 importFrom(pillar,style_subtle)
 importFrom(pillar,tbl_format_header)
+importFrom(pkgconfig,get_config)
 importFrom(plotly,plot_ly)
 importFrom(purrr,imap)
 importFrom(purrr,map)
@@ -113,17 +110,18 @@ importFrom(purrr,pmap)
 importFrom(purrr,reduce)
 importFrom(purrr,when)
 importFrom(rlang,":=")
+importFrom(rlang,.data)
 importFrom(rlang,dots_values)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
 importFrom(rlang,expr)
 importFrom(rlang,flatten_if)
-importFrom(rlang,is_empty)
 importFrom(rlang,is_spliced)
 importFrom(rlang,names2)
 importFrom(rlang,quo_is_null)
 importFrom(rlang,quo_name)
 importFrom(rlang,quo_squash)
+importFrom(stats,setNames)
 importFrom(stringr,regex)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace)

R/dplyr_methods.R

@@ -581,7 +581,8 @@ select.SummarizedExperiment <- function(.data, ...) {
     # colnames_col <- get_colnames_col(.data)
     # colnames_row <- get_rownames_col(.data)
     # colnames_assay = .data@assays@data |> names()
-  
+    
+    . <- NULL
     # Deprecation of special column names
     .cols <- enquos(..., .ignore_empty="all") %>% 
         map(~ quo_name(.x)) %>% unlist()
@@ -783,6 +784,7 @@ count.SummarizedExperiment <- function(x, ..., wt=NULL,
 #'     
 #' @importFrom ellipsis check_dots_used
 #' @importFrom dplyr pull
+#' @importFrom SummarizedExperiment assay
 #' @export
 pull.SummarizedExperiment <- function(.data, var=-1, name=NULL, ...) {
 
@@ -799,7 +801,7 @@ pull.SummarizedExperiment <- function(.data, var=-1, name=NULL, ...) {
         .data, 
         quo_name(var)
     )) {
-        .data= ping_old_special_column_into_metadata(.data)
+        .data <- ping_old_special_column_into_metadata(.data)
     }
 
     # If Ranges column not in query perform fast as_tibble
@@ -810,7 +812,7 @@ pull.SummarizedExperiment <- function(.data, var=-1, name=NULL, ...) {
 
     # Subset column annotation
     if (all(c(quo_names(var), quo_name_name) %in% colnames(colData(.data)))) {
-        return(colData(.data)[,quo_names(var)] %>%
+        return(colData(.data)[, quo_names(var)] %>%
             .[rep(1:length(.), each=nrow(.data) )])
     }
 
@@ -837,7 +839,7 @@ pull.SummarizedExperiment <- function(.data, var=-1, name=NULL, ...) {
 
             # reorder assay colnames before printing
             # Rearrange if assays has colnames and rownames
-            .data = order_assays_internally_to_be_consistent(.data)
+            .data <- order_assays_internally_to_be_consistent(.data)
 
         }
         return(assay(.data, quo_names(var)) |> as.matrix() |> as.vector())       

R/methods.R

@@ -1,3 +1,4 @@
+#' @importFrom methods getMethod
 setMethod(
     f="show",
     signature="SummarizedExperiment",
@@ -22,7 +23,8 @@ setMethod(
     }
 )
 
-setClass("tidySummarizedExperiment", contains=c("SummarizedExperiment", "RangedSummarizedExperiment"))
+setClass("tidySummarizedExperiment",
+    contains=c("SummarizedExperiment", "RangedSummarizedExperiment"))
 
 #' @name tidy
 #' @rdname tidy
@@ -54,15 +56,13 @@ tidy_ <- function(object) {
 }
 
 #' @importFrom methods as
-#'
+#' @rdname tidy
 #' @param object A SummarizedExperiment object
-#'
 #' @export
 tidy.SummarizedExperiment <- tidy_
 
 #' @importFrom methods as
-#'
+#' @rdname tidy
 #' @param object A SummarizedExperiment object
-#'
 #' @export
 tidy.RangedSummarizedExperiment <- tidy_

R/plotly_methods.R

@@ -50,7 +50,8 @@ plot_ly.tbl_df <- function(data=data.frame(), ..., type=NULL, name=NULL,
 
 #' @rdname plotly
 #' @export
-plot_ly.SummarizedExperiment <- function(data=data.frame(), ..., type=NULL, name=NULL,
+plot_ly.SummarizedExperiment <- function(data=data.frame(),
+    ..., type=NULL, name=NULL,
     color=NULL, colors=NULL, alpha=NULL,
     stroke=NULL, strokes=NULL, alpha_stroke=1,
     size=NULL, sizes=c(10, 100),

R/print_method.R

@@ -42,81 +42,24 @@ tbl_format_header.tidySummarizedExperiment <- function(x, setup, ...) {
     style_subtle(pillar___format_comment(header, width=setup$width))
 }
 
-#' Printing tibbles
-#'
-#' @description
-#' `r lifecycle::badge("maturing")`
-#'
-#' One of the main features of the `tbl_df` class is the printing:
-#'
-#' * Tibbles only print as many rows and columns as fit on one screen,
-#'   supplemented by a summary of the remaining rows and columns.
-#' * Tibble reveals the type of each column, which keeps the user informed about
-#'   whether a variable is, e.g., `<chr>` or `<fct>` (character versus factor).
-#'
-#' Printing can be tweaked for a one-off call by calling `print()` explicitly
-#' and setting arguments like `n` and `width`. More persistent control is
-#' available by setting the options described below.
-#'
-#' @inheritSection pillar::`pillar-package` Package options
-#' @section Package options:
-#'
-#' The following options are used by the tibble and pillar packages
-#' to format and print `tbl_df` objects.
-#' Used by the formatting workhorse `trunc_mat()` and, therefore,
-#' indirectly, by `print.tbl()`.
-#'
-#' * `tibble.print_max`: Row number threshold: Maximum number of rows printed.
-#'   Set to `Inf` to always print all rows.  Default: 20.
-#' * `tibble.print_min`: Number of rows printed if row number threshold is
-#'   exceeded. Default: 10.
-#' * `tibble.width`: Output width. Default: `NULL` (use `width` option).
-#' * `tibble.max_extra_cols`: Number of extra columns printed in reduced form.
-#'   Default: 100.
-#'
-
-#'
-#' @param x Object to format or print.
-#' @param ... Other arguments passed on to individual methods.
-#' @param n Number of rows to show. If `NULL`, the default, will print all rows
-#'   if less than option `tibble.print_max`. Otherwise, will print
-#'   `tibble.print_min` rows.
-#' @param width Width of text output to generate. This defaults to `NULL`, which
-#'   means use `getOption("tibble.width")` or (if also `NULL`)
-#'   `getOption("width")`; the latter displays only the columns that fit on one
-#'   screen. You can also set `options(tibble.width = Inf)` to override this
-#'   default and always print all columns.
-#' @param n_extra Number of extra columns to print abbreviated information for,
-#'   if the width is too small for the entire tibble. If `NULL`, the default,
-#'   will print information about at most `tibble.max_extra_cols` extra columns.
-#'
-#' @return Nothing
-#'
-#' @examples
-
-#' @name formatting
-NULL
-
-
-
 #' @name formatting
 #' @rdname formatting
 #' @aliases print
 #' @inherit tibble::formatting
 #' @return Prints a message to the console describing
-#'   the contents of the `tidyseurat`.
-#'
+#'   the contents of the `tidySingleCellExperiment`.
+#' 
 #' @param n_extra Number of extra columns to print abbreviated information for,
 #'   if the width is too small for the entire tibble. If `NULL`, the default,
 #'   will print information about at most `tibble.max_extra_cols` extra columns.
 #' 
 #' @examples
-#' library(dplyr)
-#' pasilla  %>% print()
+#' data(pasilla)
+#' print(pasilla)
 #' 
 #' @importFrom vctrs new_data_frame
-#' @importFrom rlang is_empty
-#' @importFrom stringr str_replace
+#' @importFrom SummarizedExperiment assayNames
+#' @importFrom stats setNames
 #' @export
 print.SummarizedExperiment <- function(x, ..., n=NULL,
     width=NULL, n_extra=NULL) {
@@ -149,9 +92,9 @@ print.SummarizedExperiment <- function(x, ..., n=NULL,
 
     my_tibble |>
         new_data_frame(class=c("tidySummarizedExperiment", "tbl")) %>%
-        add_attr( nrow(x),  "number_of_features") %>%
-        add_attr( ncol(x),  "number_of_samples") %>%
-        add_attr( assays(x) %>% names , "assay_names") %>%
+        add_attr(nrow(x),  "number_of_features") %>%
+        add_attr(ncol(x),  "number_of_samples") %>%
+        add_attr(assays(x) %>% names , "assay_names") %>%
 
     # Set fake dimensions for efficiancy
     add_attr(