From 7653d6f4f80b99df7a0ac0a7e9a07accd9ca2301 Mon Sep 17 00:00:00 2001
From: HDash <16350928+HDash@users.noreply.github.com>
Date: Tue, 25 Jun 2024 19:27:23 +0100
Subject: [PATCH] Fix examples and import conflicts

---
 DESCRIPTION         | 4 ----
 NAMESPACE           | 6 ++++++
 R/MotifPeeker.R     | 5 +++++
 R/calc_frip.R       | 2 +-
 R/check_ENCODE.R    | 2 +-
 R/link_JASPAR.R     | 4 ----
 R/print_DT.R        | 2 ++
 man/calc_frip.Rd    | 2 +-
 man/check_ENCODE.Rd | 2 +-
 man/link_JASPAR.Rd  | 5 -----
 man/print_DT.Rd     | 3 +++
 11 files changed, 20 insertions(+), 17 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3d78593..52a9528 100644
--- a/DESCRIPTION
+++ b/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
diff --git a/NAMESPACE b/NAMESPACE
index 8c66a57..5395bd2 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,10 @@ 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)
@@ -18,6 +22,7 @@ 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)
diff --git a/R/MotifPeeker.R b/R/MotifPeeker.R
index b1ee3d8..472bab0 100644
--- a/R/MotifPeeker.R
+++ b/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.
 #' 
diff --git a/R/calc_frip.R b/R/calc_frip.R
index 812b083..2b221ba 100644
--- a/R/calc_frip.R
+++ b/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(
diff --git a/R/check_ENCODE.R b/R/check_ENCODE.R
index a934142..8db9eef 100644
--- a/R/check_ENCODE.R
+++ b/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) {
diff --git a/R/link_JASPAR.R b/R/link_JASPAR.R
index abb8996..159a768 100644
--- a/R/link_JASPAR.R
+++ b/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")) {
diff --git a/R/print_DT.R b/R/print_DT.R
index 838a6e2..94cdb9f 100644
--- a/R/print_DT.R
+++ b/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
diff --git a/man/calc_frip.Rd b/man/calc_frip.Rd
index fa9a127..20d0389 100644
--- a/man/calc_frip.Rd
+++ b/man/calc_frip.Rd
@@ -34,6 +34,6 @@ read_file <- system.file("extdata", "CTCF_ChIP_alignment.bam",
 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)
 
 }
diff --git a/man/check_ENCODE.Rd b/man/check_ENCODE.Rd
index d3df7c9..50d3edb 100644
--- a/man/check_ENCODE.Rd
+++ b/man/check_ENCODE.Rd
@@ -25,6 +25,6 @@ Check and get files from ENCODE project. Requires the input to be in ENCODE
 ID format. Uses BiocFileCache to cache downloads. Only works for files.
 }
 \examples{
-check_ENCODE("ENCFF109VAD")
+check_ENCODE("ENCFF109VAD", expect_format = "bam")
 
 }
diff --git a/man/link_JASPAR.Rd b/man/link_JASPAR.Rd
index 901d847..c7e3396 100644
--- a/man/link_JASPAR.Rd
+++ b/man/link_JASPAR.Rd
@@ -18,10 +18,5 @@ A character string containing the JASPAR motif link. If
 }
 \description{
 Get JASPAR link for motifs
-}
-\examples{
-link_JASPAR("MA1930.2")
-link_JASPAR("MA1930.2", download = TRUE)
-
 }
 \keyword{internal}
diff --git a/man/print_DT.Rd b/man/print_DT.Rd
index 88f9df0..0edd29b 100644
--- a/man/print_DT.Rd
+++ b/man/print_DT.Rd
@@ -14,6 +14,9 @@ print_DT(df, html_tags = FALSE, extra = FALSE)
 \item{extra}{Logical. If TRUE, adds extra options like search to the
 datatable.}
 }
+\value{
+A DT object suitable to be used with \code{print()}.
+}
 \description{
 Print DT table
 }