fix: no more reexports, attach tidyverse packages on load, tidy up expand and as_tibble methods

Author: js2264

DESCRIPTION

@@ -35,6 +35,7 @@ Imports:
     rtracklayer,
     methods,
     tidyr, 
+    tibble, 
     ggplot2,
     ggrastr, 
     dplyr,

NAMESPACE

@@ -7,15 +7,11 @@ S3method(print,CoverageExperiment)
 S3method(tbl_format_header,tidyAggregatedCoverage)
 S3method(tbl_format_header,tidyCoverageExperiment)
 export(CoverageExperiment)
-export(aggregate)
-export(as_tibble)
 export(coarsen)
-export(expand)
 export(geom_aggrcoverage)
 export(geom_coverage)
 export(scale_x_genome)
 export(scale_y_coverage)
-export(show)
 exportMethods(CoverageExperiment)
 exportMethods(aggregate)
 exportMethods(coarsen)
@@ -57,4 +53,5 @@ importFrom(tidyr,all_of)
 importFrom(tidyr,any_of)
 importFrom(tidyr,expand)
 importFrom(tidyr,pivot_longer)
+importFrom(utils,packageDescription)
 importFrom(vctrs,new_data_frame)

R/as_tibble.R

@@ -2,10 +2,9 @@
 #' 
 #' Coerce an `CoverageExperiment` or `AggregatedCoverage` object into a `tibble`
 #' 
-#' @name as_tibble-methods
-#' @rdname as_tibble-methods
-#' @param x an `CoverageExperiment` object
-#' @param ... ignored
+#' @name as_tibble-AggregatedCoverage
+#' @rdname as_tibble-AggregatedCoverage
+#' @inherit tibble::as_tibble
 #' @return `tibble`
 #' 
 #' @importFrom tidyr any_of
@@ -17,7 +16,8 @@
 #' as_tibble(ac)
 NULL
 
-#' @rdname as_tibble-methods
+#' @rdname as_tibble-AggregatedCoverage
+#' @method as_tibble AggregatedCoverage
 #' @export
 
 as_tibble.AggregatedCoverage <- function(x, ...) {

R/attach.R

@@ -0,0 +1,21 @@
+core <- c("dplyr", "tidyr", "ggplot2")
+
+core_unloaded <- function() {
+    search <- paste0("package:", core)
+    core[!search %in% search()]
+}
+
+same_library <- function(pkg) {
+    loc <- if (pkg %in% loadedNamespaces()) 
+        dirname(getNamespaceInfo(pkg, "path"))
+    library(pkg, lib.loc=loc, character.only=TRUE, warn.conflicts=FALSE)
+}
+
+tidyverse_attach <- function() {
+    to_load <- core_unloaded()
+    
+    suppressPackageStartupMessages(
+        lapply(to_load, same_library))
+    
+    invisible(to_load)
+}

R/expand.R

@@ -8,22 +8,21 @@
 #' object into a long data frame, and adds the `ranges` 
 #' and `seqnames` to the resulting `tibble`. 
 #' 
-#' @name expand,CoverageExperiment
-#' @aliases expand,CoverageExperiment-method
-#' @rdname expand
-#' 
-#' @param data a `CoverageExperiment` object
-#' @param ...,.name_repair ignored
+#' @name expand-CoverageExperiment
+#' @rdname expand-CoverageExperiment
+#' @inherit tidyr::expand
 #' @return a `tibble` object
 #' 
 #' @importFrom tidyr expand
-#' @export
 #' @examples 
 #' data(ce)
 #' ce
-#' 
 #' expand(ce)
+NULL
 
+#' @rdname expand-CoverageExperiment
+#' @method expand CoverageExperiment
+#' @export
 expand.CoverageExperiment <- function(data, ..., .name_repair = NULL) {
     tracks <- colData(data)$track
     features <- rowData(data)$features

R/reexports.R

@@ -1,8 +1,6 @@
-#' show
+#' @title show method for `CoverageExperiment` and `AggregatedCoverage` objects
 #' 
-#' show method for `CoverageExperiment` and `AggregatedCoverage` objects
-#' 
-#' @name show
+#' @name show-tidyCoverage
 #' @aliases show,CoverageExperiment-method
 #' @aliases show,AggregatedCoverage-method
 #' 
@@ -20,9 +18,7 @@
 #' @importFrom vctrs new_data_frame
 #' @importFrom SummarizedExperiment assayNames
 #' @importFrom stats setNames
-#' @export
 #' 
-#' @inherit tibble::formatting
 #' @return `Prints a message to the console describing
 #' the contents of the `CoverageExperiment` or `AggregatedCoverage` objects.
 #' @examples
@@ -32,7 +28,8 @@
 #' print(ac)
 NULL
 
-#' @name show
+#' @method show CoverageExperiment
+#' @aliases show,CoverageExperiment-method
 #' @export
 
 setMethod("show", signature("CoverageExperiment"), function(object) {
@@ -52,7 +49,8 @@ setMethod("show", signature("CoverageExperiment"), function(object) {
     }
 })
 
-#' @name show
+#' @method show AggregatedCoverage
+#' @aliases show,AggregatedCoverage-method
 #' @export
 
 setMethod("show", signature("AggregatedCoverage"), function(object) {
@@ -74,7 +72,7 @@ setMethod("show", signature("AggregatedCoverage"), function(object) {
     }
 })
 
-#' @name show
+#' @method print CoverageExperiment
 #' @export
 
 print.CoverageExperiment <- function (x, ..., n = NULL) {
@@ -105,7 +103,7 @@ print.CoverageExperiment <- function (x, ..., n = NULL) {
     }
 }
 
-#' @name show
+#' @method print AggregatedCoverage
 #' @export
 
 print.AggregatedCoverage <- function (x, ..., n = NULL) {
@@ -136,7 +134,7 @@ print.AggregatedCoverage <- function (x, ..., n = NULL) {
     }
 }
 
-#' @name show
+#' @method tbl_format_header tidyCoverageExperiment
 #' @export
 
 tbl_format_header.tidyCoverageExperiment <- function(x, setup, ...) {
@@ -170,7 +168,7 @@ tbl_format_header.tidyCoverageExperiment <- function(x, setup, ...) {
     pillar::style_subtle(.pillar___format_comment(header, width=setup$width))
 }
 
-#' @name show
+#' @method tbl_format_header tidyAggregatedCoverage
 #' @export
 
 tbl_format_header.tidyAggregatedCoverage <- function(x, setup, ...) {

R/show.R

@@ -0,0 +1,37 @@
+#' tidyCoverage: Tidyomics-based analysis of coverage tracks over genomic features
+#'
+#' @description
+#' The tidyCoverage package provides a bridge between Bioconductor
+#' SummarizedExperiment objects and the tidyomics project. 
+#' 
+#' @references
+#' Serizay J, Koszul R., Epigenomics coverage data extraction and aggregation 
+#' in R with tidyCoverage. Bioinformatics 40, btae487 (2024).
+#' \doi{10.1093/bioinformatics/btae487}
+#'
+#' @seealso
+#' Useful links:
+#' \itemize{
+#'   \item \url{https://github.com/js2264/tidyCoverage}
+#'   \item Report bugs at \url{https://github.com/js2264/tidyCoverage/issues}
+#' }
+#'
+#' @author Jacques Serizay 
+#'
+#' @docType package
+#' @name tidyCoverage-package
+#' @aliases tidyCoverage
+#' @keywords internal
+"_PACKAGE"
+
+#' @importFrom utils packageDescription
+.onAttach <- function(libname, pkgname) {
+    attached <- tidyverse_attach()
+    
+    # Print loading message about printing
+    cli::cli_alert_info(paste0(
+        "tidyCoverage says: The tidy printing is now handled externally.\n",
+        "If you want to visualize the data in a tidy way, do `library(tidyprint)`.\n",
+        "See `https://github.com/tidyomics/tidyprint` for more information."
+    ))
+}