Merge pull request #5 from neurogenomics/remove_donttest

Remove donttest
neurogenomics · Nov 6, 2024 · 8758def · 8758def
2 parents 66d666f + bfa2514
commit 8758def
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diff --git a/.github/workflows/rworkflows_nomeme.yml b/.github/workflows/rworkflows_nomeme.yml
@@ -0,0 +1,50 @@
+name: rworkflows_nomeme
+'on':
+  push:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+    - '*'
+    - '!gh-pages'
+  pull_request:
+    branches:
+    - master
+    - main
+    - devel
+    - RELEASE_**
+    - '*'
+    - '!gh-pages'
+jobs:
+  rworkflows:
+    permissions: write-all
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+    container: ${{ matrix.config.cont }}
+    strategy:
+      fail-fast: ${{ false }}
+      matrix:
+        config:
+        - os: ubuntu-latest
+          bioc: devel
+          r: auto
+          cont: bioconductor/bioconductor_docker:devel # No MEME Suite install
+          rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+        - os: macOS-latest
+          r: latest
+          bioc: release
+    steps:
+    - uses: HDash/rworkflows@master
+      with:
+        run_bioccheck: ${{ true }}
+        run_rcmdcheck: ${{ true }}
+        as_cran: ${{ true }}
+        run_vignettes: ${{ true }}
+        has_testthat: ${{ true }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
+        has_runit: ${{ false }}
+        has_latex: ${{ false }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run_docker: ${{ false }}
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: MotifPeeker
 Title: Benchmarking Epigenomic Profiling Methods Using Motif Enrichment
-Version: 0.99.7
+Version: 0.99.8
 Authors@R: c( 
     person(given = "Hiranyamaya",
            family = "Dash",

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,7 +13,6 @@ export(get_df_distances)
 export(get_df_enrichment)
 export(motif_enrichment)
 export(motif_similarity)
-export(plot_enrichment_overall)
 export(read_motif_file)
 export(read_peak_file)
 export(save_peak_file)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,11 @@
+# MotifPeeker 0.99.8
+
+## Miscellaneous
+
+* Optimise examples and remove `\donttest{}` blocks.
+* Add GitHub Actions for rworkflows without MEME Suite.
+
+
 # MotifPeeker 0.99.7
 
 ## New Features

diff --git a/R/MotifPeeker.R b/R/MotifPeeker.R
@@ -151,9 +151,7 @@
 #'                 package = "MotifPeeker")
 #' )
 #' 
-#' \donttest{
-#'     if (memes::meme_is_installed()) {
-#'     # MotifPeeker takes time to run
+#' if (memes::meme_is_installed()) {
 #'     MotifPeeker(
 #'         peak_files = peaks,
 #'         reference_index = 1,
@@ -173,7 +171,6 @@
 #'         quiet = TRUE,
 #'         verbose = FALSE
 #'     )
-#'     }
 #' }
 #' 
 #' @export

diff --git a/R/denovo_motifs.R b/R/denovo_motifs.R
@@ -45,10 +45,12 @@
 #'     genome_build <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
 #'    
 #'     res <- denovo_motifs(list(CTCF_TIP_peaks),
-#'                         trim_seq_width = 100,
+#'                         trim_seq_width = 50,
 #'                         genome_build = genome_build,
-#'                         denovo_motifs = 2,
+#'                         denovo_motifs = 1,
 #'                         filter_n = 6,
+#'                         minw = 8,
+#'                         maxw = 8,
 #'                         out_dir = tempdir())
 #'     print(res[[1]]$consensus)
 #' }

diff --git a/R/find_motifs.R b/R/find_motifs.R
@@ -21,25 +21,23 @@
 #' @inherit memes::runTomTom return
 #' 
 #' @examples
-#' data("CTCF_TIP_peaks", package = "MotifPeeker")
+#' if (memes::meme_is_installed()) {
+#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
 #'     
-#' \donttest{
-#'     if (memes::meme_is_installed()) {
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
 #'    
 #'         res <- denovo_motifs(list(CTCF_TIP_peaks),
-#'                         trim_seq_width = 100,
+#'                         trim_seq_width = 50,
 #'                         genome_build = genome_build,
-#'                         denovo_motifs = 2,
-#'                         filter_n = 6,
+#'                         denovo_motifs = 1,
+#'                         filter_n = 10,
 #'                         out_dir = tempdir())
 #'         res2 <- find_motifs(res, motif_db = get_JASPARCORE(),
 #'                             out_dir = tempdir())
 #'         print(res2)
 #'     }
-#'     }
 #' }
 #' 
 #' @export

diff --git a/R/get_df_distances.R b/R/get_df_distances.R
@@ -85,7 +85,7 @@ get_df_distances <- function(result,
                 exp_label = exp_label_combinations[i],
                 exp_type = exp_type_combinations[i],
                 motif_indice = rep(seq_len(motif_len), result_len)[i],
-                distance = MotifPeeker::summit_to_motif(
+                distance = summit_to_motif(
                     peak, motif,
                     genome_build = genome_build,
                     out_dir = file.path(out_dir, "fimo", i),

diff --git a/R/get_df_enrichment.R b/R/get_df_enrichment.R
@@ -27,25 +27,24 @@
 #' 
 #' @examples
 #' if (memes::meme_is_installed()) {
-#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
-#' data("CTCF_TIP_peaks", package = "MotifPeeker")
-#' data("motif_MA1102.3", package = "MotifPeeker")
-#' data("motif_MA1930.2", package = "MotifPeeker")
-#' input <- list(
-#'     peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
-#'     exp_type = c("ChIP", "TIP"),
-#'     exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
-#'     read_count = c(150, 200),
-#'     peak_count = c(100, 120)
-#' )
-#' segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
-#' motifs <- list(
-#'     motifs = list(motif_MA1930.2, motif_MA1102.3),
-#'     motif_labels = list("MA1930.2", "MA1102.3")
-#' )
-#' reference_index <- 1
+#'     data("CTCF_ChIP_peaks", package = "MotifPeeker")
+#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
+#'     data("motif_MA1102.3", package = "MotifPeeker")
+#'     data("motif_MA1930.2", package = "MotifPeeker")
+#'     input <- list(
+#'         peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
+#'         exp_type = c("ChIP", "TIP"),
+#'         exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
+#'         read_count = c(150, 200),
+#'         peak_count = c(100, 120)
+#'     )
+#'     segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
+#'     motifs <- list(
+#'         motifs = list(motif_MA1930.2, motif_MA1102.3),
+#'         motif_labels = list("MA1930.2", "MA1102.3")
+#'     )
+#'     reference_index <- 1
 #' 
-#' \donttest{
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
@@ -56,7 +55,6 @@
 #'         )
 #'     }
 #' }
-#' }
 #' 
 #' @family generate data.frames
 #' 
@@ -89,7 +87,7 @@ get_df_enrichment <- function(result,
         function(i) {
             peak <- peak_combinations[[i]]
             motif <- motif_combinations[[i]]
-            res <- MotifPeeker::motif_enrichment(
+            res <- motif_enrichment(
                 peak, motif,
                 genome_build = genome_build,
                 out_dir = file.path(out_dir, "ame_all", i),

diff --git a/R/motif_enrichment.R b/R/motif_enrichment.R
@@ -20,24 +20,23 @@
 #' @importFrom memes runAme
 #' @importFrom utils read.table
 #'
-#' @returns A list containing a FIMO results data frame and a numeric referring
+#' @returns A list containing a AME results data frame and a numeric referring
 #' to the proportion of peaks with a motif.
 #'
 #' @examples
 #' if (memes::meme_is_installed()) {
-#' data("CTCF_TIP_peaks", package = "MotifPeeker")
-#' data("motif_MA1102.3", package = "MotifPeeker")
+#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
+#'     data("motif_MA1102.3", package = "MotifPeeker")
 #' 
-#' \donttest{
 #'     res <- motif_enrichment(
 #'         peak_input = CTCF_TIP_peaks,
 #'         motif = motif_MA1102.3,
 #'         genome_build =
-#'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
+#'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38,
+#'         
 #'     )
 #'     print(res)
 #' }
-#' }
 #'
 #' @seealso \code{\link[memes]{runAme}}
 #' 
@@ -66,8 +65,8 @@ motif_enrichment <- function(peak_input,
     peak_sequences <- BSgenome::getSeq(genome_build, peak_input)
 
     ## Generate 0-order background model from the input sequences
-    bfile <- markov_background_model(sequences = peak_sequences,
-                                    out_dir = out_dir)
+    # bfile <- markov_background_model(sequences = peak_sequences,
+    #                                 out_dir = out_dir)
     ame_out <- memes::runAme(peak_sequences,
                             database = list(motif),
                             outdir = out_dir,

diff --git a/R/motif_similarity.R b/R/motif_similarity.R
@@ -32,25 +32,25 @@
 #' 
 #' @examples
 #' if (memes::meme_is_installed()) {
-#' data("CTCF_TIP_peaks", package = "MotifPeeker")
-#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
+#'     data("CTCF_TIP_peaks", package = "MotifPeeker")
+#'     data("CTCF_ChIP_peaks", package = "MotifPeeker")
 #' 
-#' \donttest{
 #'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38")) {
 #'         genome_build <-
 #'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
 #'         segregated_peaks <- segregate_seqs(CTCF_TIP_peaks, CTCF_ChIP_peaks)
 #'         denovo_motifs <- denovo_motifs(unlist(segregated_peaks),
-#'                             trim_seq_width = 100,
+#'                             trim_seq_width = 50,
 #'                             genome_build = genome_build,
-#'                             denovo_motifs = 2,
+#'                             denovo_motifs = 1,
 #'                             filter_n = 6,
+#'                             maxw = 8,
+#'                             minw = 8,
 #'                             out_dir = tempdir())
 #'         similarity_matrices <- motif_similarity(denovo_motifs)
 #'         print(similarity_matrices)
 #'     }
 #' }
-#' }
 #' 
 #' @export
 motif_similarity <- function(streme_out,

diff --git a/R/plot_enrichment_individual.R b/R/plot_enrichment_individual.R
@@ -23,44 +23,6 @@
 #' \code{html_tags} is \code{TRUE}, the function returns a \code{tagList} object
 #' instead.
 #' 
-#' @examples
-#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
-#' data("CTCF_TIP_peaks", package = "MotifPeeker")
-#' data("motif_MA1102.3", package = "MotifPeeker")
-#' data("motif_MA1930.2", package = "MotifPeeker")
-#' input <- list(
-#'     peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
-#'     exp_type = c("ChIP", "TIP"),
-#'     exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
-#'     read_count = c(150, 200),
-#'     peak_count = c(100, 120)
-#' )
-#' segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
-#' motifs <- list(
-#'     motifs = list(motif_MA1930.2, motif_MA1102.3),
-#'     motif_labels = list("MA1930.2", "MA1102.3")
-#' )
-#'     
-#' \donttest{
-#'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38") &&
-#'         memes::meme_is_installed()) {
-#'         genome_build <-
-#'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
-#'         enrichment_df <- get_df_enrichment(
-#'             input, segregated_input, motifs, genome_build,
-#'             reference_index = 1
-#'         )
-#'         label_colours <- c("red", "cyan")
-#'     
-#'         plt <- MotifPeeker:::plot_enrichment_individual(
-#'             input, enrichment_df, comparison_i = 2, motif_i = 1,
-#'             label_colours = label_colours, reference_index = 1,
-#'             html_tags = FALSE
-#'         )
-#'         print(plt)
-#'     }
-#' }
-#' 
 #' @family plot functions
 #' 
 #' @keywords internal

diff --git a/R/plot_enrichment_overall.R b/R/plot_enrichment_overall.R
@@ -21,47 +21,9 @@
 #'  \item{\code{$perc_plt}}{y-axis represents the percentage of peaks.}
 #' }
 #' 
-#' @examples
-#' data("CTCF_ChIP_peaks", package = "MotifPeeker")
-#' data("CTCF_TIP_peaks", package = "MotifPeeker")
-#' data("motif_MA1102.3", package = "MotifPeeker")
-#' data("motif_MA1930.2", package = "MotifPeeker")
-#' input <- list(
-#'     peaks = list(CTCF_ChIP_peaks, CTCF_TIP_peaks),
-#'     exp_type = c("ChIP", "TIP"),
-#'     exp_labels = c("CTCF_ChIP", "CTCF_TIP"),
-#'     read_count = c(150, 200),
-#'     peak_count = c(100, 120)
-#' )
-#' segregated_input <- segregate_seqs(input$peaks[[1]], input$peaks[[2]])
-#' motifs <- list(
-#'     motifs = list(motif_MA1930.2, motif_MA1102.3),
-#'     motif_labels = list("MA1930.2", "MA1102.3")
-#' )
-#'     
-#' \donttest{
-#'     if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38") &&
-#'         memes::meme_is_installed()) {
-#'         genome_build <-
-#'             BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
-#'         enrichment_df <- get_df_enrichment(
-#'             input, segregated_input, motifs, genome_build,
-#'             reference_index = 1
-#'         )
-#'         label_colours <- c("red", "cyan")
-#'     
-#'         plt <- plot_enrichment_overall(
-#'         enrichment_df, motif_i = 1, label_colours = label_colours,
-#'         reference_label = "CTCF_ChIP", html_tags = FALSE
-#'         )
-#'         print(plt$count_plot)
-#'         print(plt$perc_plot)
-#'     }
-#' }
-#' 
 #' @family plot functions
 #' 
-#' @export
+#' @keywords internal
 plot_enrichment_overall <- function(enrichment_df,
                                     motif_i,
                                     label_colours,

diff --git a/R/utilities.R b/R/utilities.R
@@ -145,7 +145,7 @@ use_cache <- function(url, verbose = FALSE) {
 #' @keywords internal
 check_duplicates <- function(x) {
     stp_msg <- paste("Duplicated items found in the label list. Please input",
-                     "unique experiment and motif labels.")
+                    "unique experiment and motif labels.")
     if (any(duplicated(x))) {
         stop(stp_msg)
     }