Fix examples and import conflicts

DESCRIPTION

@@ -39,9 +39,7 @@ Imports:
     BiocParallel,
     DT,
     ggplot2,
-    patchwork,
     plotly,
-    scales,
     tidyverse,
     universalmotif,
     GenomicRanges,
@@ -52,7 +50,6 @@ Imports:
     rmarkdown,
     curl,
     jsonlite,
-    htmltools,
     viridis,
     emoji,
     SummarizedExperiment,
@@ -68,7 +65,6 @@ Suggests:
     markdown,
     methods,
     remotes,
-    rmarkdown,
     rworkflows,
     testthat (>= 3.0.0),
     utils

NAMESPACE

@@ -11,13 +11,18 @@ export(read_motif_file)
 export(read_peak_file)
 export(report_command)
 export(report_header)
+import(ggplot2)
+import(plotly, except = last_plot)
+
+import(tidyverse)
 importFrom(BiocFileCache,BiocFileCache)
 importFrom(BiocFileCache,bfcinfo)
 importFrom(DT,datatable)
 importFrom(GenomicAlignments,summarizeOverlaps)
 importFrom(Rsamtools,countBam)
 importFrom(SummarizedExperiment,assay)
 importFrom(curl,curl_fetch_memory)
+importFrom(emoji,emoji)
 importFrom(htmltools,tagList)
 importFrom(htmlwidgets,JS)
 importFrom(jsonlite,fromJSON)
@@ -30,3 +35,4 @@ importFrom(universalmotif,read_meme)
 importFrom(universalmotif,read_transfac)
 importFrom(universalmotif,read_uniprobe)
 importFrom(utils,browseURL)
+importFrom(viridis,scale_fill_viridis)

R/MotifPeeker.R

@@ -89,9 +89,14 @@
 #' @inheritParams read_motif_file
 #' @inheritParams check_genome_build
 #' 
+#' @import ggplot2
+#' @import tidyverse
+#' @importFrom emoji emoji
+#' @importFrom viridis scale_fill_viridis
 #' @importFrom tools file_path_sans_ext
 #' @importFrom rmarkdown render
 #' @importFrom utils browseURL
+#' @rawNamespace import(plotly, except = last_plot)
 #' 
 #' @return Path to the output directory.
 #' 

R/calc_frip.R

@@ -25,7 +25,7 @@
 #' read_file <- Rsamtools::BamFile(read_file)
 #' data("CTCF_ChIP_peaks", package = "MotifPeeker")
 #' 
-#' frip(read_file, CTCF_ChIP_peaks)
+#' calc_frip(read_file, CTCF_ChIP_peaks)
 #' 
 #' @export
 calc_frip <- function(

R/check_ENCODE.R

@@ -16,7 +16,7 @@
 #' @importFrom jsonlite fromJSON
 #' 
 #' @examples
-#' check_ENCODE("ENCFF109VAD")
+#' check_ENCODE("ENCFF109VAD", expect_format = "bam")
 #' 
 #' @export
 check_ENCODE <- function(encode_id, expect_format, verbose = FALSE) {

R/link_JASPAR.R

@@ -7,10 +7,6 @@
 #' @returns A character string containing the JASPAR motif link. If
 #' \code{motif_id} is not a valid JASPAR motif ID, it is returned as is.
 #' 
-#' @examples
-#' link_JASPAR("MA1930.2")
-#' link_JASPAR("MA1930.2", download = TRUE)
-#' 
 #' @keywords internal
 link_JASPAR <- function(motif_id, download = FALSE) {
     if (is.na(motif_id) || !startsWith(motif_id, "MA")) {

R/print_DT.R

@@ -9,6 +9,8 @@
 #' @importFrom htmlwidgets JS
 #' @importFrom htmltools tagList
 #' 
+#' @returns A DT object suitable to be used with \code{print()}.
+#' 
 #' @keywords internal
 print_DT <- function(df, html_tags = FALSE, extra = FALSE) {
     ## Handle empty values