Merge pull request #1 from neurogenomics/bioc_review

Bioc review fix 1

.github/workflows/rworkflows.yml

@@ -6,12 +6,16 @@ name: rworkflows
     - main
     - devel
     - RELEASE_**
+    - '*'
+    - '!gh-pages'
   pull_request:
     branches:
     - master
     - main
     - devel
     - RELEASE_**
+    - '*'
+    - '!gh-pages'
 jobs:
   rworkflows:
     permissions: write-all

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: MotifPeeker
 Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
-Version: 0.99.4
+Version: 0.99.5
 Authors@R: c( 
     person(given = "Hiranyamaya",
            family = "Dash",
@@ -57,7 +57,6 @@ Imports:
     BSgenome,
     memes,
     S4Vectors,
-    magrittr,
     dplyr,
     purrr,
     tidyr,

NAMESPACE

@@ -2,31 +2,23 @@
 
 export("%>%")
 export(MotifPeeker)
-export(bpapply)
 export(calc_frip)
 export(check_ENCODE)
 export(check_JASPAR)
 export(check_genome_build)
 export(denovo_motifs)
 export(find_motifs)
-export(format_exptype)
 export(get_JASPARCORE)
 export(get_df_distances)
 export(get_df_enrichment)
 export(motif_enrichment)
 export(motif_similarity)
-export(plot_enrichment_individual)
 export(plot_enrichment_overall)
-export(pretty_number)
 export(read_motif_file)
 export(read_peak_file)
-export(report_command)
-export(report_header)
 export(save_peak_file)
 export(segregate_seqs)
 export(summit_to_motif)
-export(to_plotly)
-export(trim_seqs)
 import(BiocParallel)
 import(dplyr)
 import(ggplot2)
@@ -55,10 +47,10 @@ importFrom(Rsamtools,countBam)
 importFrom(S4Vectors,queryHits)
 importFrom(S4Vectors,subjectHits)
 importFrom(SummarizedExperiment,assay)
+importFrom(dplyr,"%>%")
 importFrom(heatmaply,heatmaply)
 importFrom(htmltools,tagList)
 importFrom(htmlwidgets,JS)
-importFrom(magrittr,"%>%")
 importFrom(memes,meme_is_installed)
 importFrom(memes,runAme)
 importFrom(memes,runFimo)

NEWS.md

@@ -1,3 +1,15 @@
+# MotifPeeker 0.99.5
+
+## Miscellaneous
+
+* Replace `magrittr` import by `dplyr::%>%`.
+* Reduce the number of exported functions.
+* Move utility functions to 'utilities.R'.
+* Allow vignettes to run without MEME suite installed.
+* Remove `stopper()` wrapper around `stop()`.
+* Use message() for parallel executions
+
+
 # MotifPeeker 0.99.4
 
 ## Miscellaneous

R/MotifPeeker.R

@@ -207,18 +207,18 @@ MotifPeeker <- function(
         len_alignment_files <- if (is.list(alignment_files))
             length(alignment_files) else 1
         if (len_peak_files != len_alignment_files) {
-            stopper(stp_msg)
+            stop(stp_msg)
         }
     }
     if (!is.null(cell_counts) && length(cell_counts) != length(peak_files)) {
         stp_msg <- paste0("Length of ", shQuote("cell_counts"), " must be ",
         "equal to ", shQuote("peak_files"), ".")
-        stopper(stp_msg)
+        stop(stp_msg)
     }
     if (denovo_motif_discovery &&
         (is.null(denovo_motifs) || denovo_motifs < 1)) {
         stp_msg <- "Number of de-novo motifs to find must be greater than 0."
-        stopper(stp_msg)
+        stop(stp_msg)
     }
 
     ### Check duplicate labels ###
@@ -233,7 +233,7 @@ MotifPeeker <- function(
     ### Create output folder ###
     if (!dir.exists(out_dir)) {
         stp_msg <- "Output directory does not exist."
-        stopper(stp_msg)
+        stop(stp_msg)
     }
     out_dir <- file.path(
         out_dir,

R/bpapply.R

@@ -19,10 +19,10 @@
 #' half_it <- function(arg1) return(arg1 / 2)
 #' x <- seq_len(10)
 #' 
-#' res <- bpapply(x, half_it, workers = 2)
+#' res <- MotifPeeker:::bpapply(x, half_it, workers = 2)
 #' print(res)
 #' 
-#' @export
+#' @keywords internal
 bpapply <- function(
         X,
         FUN,
@@ -36,7 +36,7 @@ bpapply <- function(
     stp_msg <- paste("Supplied apply_fun is not a valid BiocParallel function.")
     apply_fun_package <- attr(apply_fun, "package")
     if (length(apply_fun_package) == 0 ||
-        apply_fun_package != "BiocParallel")  stopper(stp_msg)
+        apply_fun_package != "BiocParallel")  stop(stp_msg)
 
     BPPARAM <- get_bpparam(workers = workers,
                             progressbar = progressbar,

R/check_ENCODE.R

@@ -38,14 +38,14 @@ check_ENCODE <- function(encode_id, expect_format, verbose = FALSE) {
     if (!grepl(id_pattern, json_data$accession) || is.null(json_data$href)) {
         stp_msg <- paste("Error downloading ENCODE JSON data.",
                             "Check if ID is correct and leads to a file.")
-        stopper(stp_msg)
+        stop(stp_msg)
     }
     ext <- basename(tools::file_ext(json_data$href))
     if (!ext %in% expect_format) {
         stp_msg <- paste0("Error downloading file from ENCODE.\n",
                             "Expected file format: ", expect_format,
                             " but got: ", ext)
-        stopper(stp_msg)
+        stop(stp_msg)
     }
 
     ### Fetch file ###

R/check_genome_build.R

@@ -34,5 +34,5 @@ check_genome_build <- function(genome_build) {
         ". ",
         "Try passing a BSgenome object."
     )
-    stopper(stp_msg)
+    stop(stp_msg)
 }

R/download_button.R

@@ -27,37 +27,29 @@ download_button <- function(path,
                             icon = "fa fa-save",
                             add_button = TRUE,
                             ...) {
-    if (add_button) {
-        wrn_msg <- paste("Package", shQuote("downloadthis"), "is required to",
-                        "add download buttons to the HTML report. Skipping",
-                        "download buttons...")
-        check_dep("downloadthis", fatal = FALSE, custom_msg = wrn_msg)
-
-        type <- tolower(type)
-        if (type == "dir") {
-            btn <- downloadthis::download_dir(
-                path = path,
-                output_name = output_name,
-                button_label = button_label,
-                button_type = button_type,
-                has_icon = has_icon,
-                icon = icon,
-                self_contained = TRUE
-            )
-        } else if (type == "file") {
-            btn <- downloadthis::download_file(
-                path = path,
-                output_name = output_name,
-                button_label = button_label,
-                button_type = button_type,
-                has_icon = has_icon,
-                icon = icon,
-                self_contained = TRUE
-            )
-        }
-
-        return(btn)
-    } else {
-        return(invisible())
-    }
+    if (!add_button) return(invisible())
+
+    wrn_msg <- paste("Package", shQuote("downloadthis"), "is required to",
+                    "add download buttons to the HTML report. Skipping",
+                    "download buttons...")
+    check_dep("downloadthis", fatal = FALSE, custom_msg = wrn_msg)
+
+    btn_args <- list(
+        path = path,
+        output_name = output_name,
+        button_label = button_label,
+        button_type = button_type,
+        has_icon = has_icon,
+        icon = icon,
+        self_contained = TRUE
+    )
+
+    type <- tolower(type)
+    btn <- switch(
+        type,
+        "dir" = do.call(downloadthis::download_dir, btn_args),
+        "file" = do.call(downloadthis::download_file, btn_args)
+    )
+
+    return(btn)
 }

R/dt_enrichment_individual.R

@@ -15,7 +15,7 @@ dt_enrichment_individual <- function(result,
                                     motif_i,
                                     reference_index = 1) {
     stp_msg <- "reference_index cannot be the same as comparison_i."
-    if (reference_index == comparison_i) stopper(stp_msg)
+    if (reference_index == comparison_i) stop(stp_msg)
 
     ref_label <- result$exp_labels[reference_index]
     comp_label <- result$exp_labels[comparison_i]

R/filter_repeats.R

@@ -17,20 +17,12 @@ filter_repeats <- function(motifs, filter_n = 6) {
     if (is.null(filter_n) || filter_n < 1) return(motifs)
 
     if (filter_n < 4) {
-        warn_msg <- paste("It is not recommended to filter out motifs with",
-        "less than 4 consecutive nucleotide repeats.")
+        warn_msg <- "It is not recommended to filter out motifs with less than 4 consecutive nucleotide repeats."
         warning(warn_msg)
     }
 
     repeat_pattern <- paste0("([A-Z])\\1{", filter_n - 1, ",}")
-    good_motif_indices <- vapply(seq_along(motifs$consensus), function(i) {
-        if (!grepl(repeat_pattern, motifs$consensus[i])) {
-            return(i)
-        } else {
-            return(-1)
-        }
-    }, numeric(1))
-    good_motif_indices <- good_motif_indices[good_motif_indices != -1]
+    good_motif_indices <- grep(repeat_pattern, motifs$consensus, invert = TRUE)
     filtered_motifs <- motifs[good_motif_indices,]
     return(filtered_motifs)
 }

R/get_df_distances.R

@@ -26,7 +26,7 @@
 #' 
 #' @importFrom purrr map_df
 #' 
-#' @return A \code{data.frame} with the following columns:
+#' @returns A \code{data.frame} with the following columns:
 #' \describe{
 #'  \item{exp_label}{Experiment labels.}
 #'  \item{exp_type}{Experiment types.}