Normalise all input paths before passing to rmarkdown::render()

R/MotifPeeker.R

@@ -176,11 +176,15 @@ MotifPeeker <- function(
     force(genome_build)
 
     ### Check argument lengths ###
-    if (!is.null(alignment_files) &&
-        length(peak_files) != length(alignment_files)) {
+    if (!is.null(alignment_files)) {
         stp_msg <- paste("Length of", shQuote("peak_files"), "and",
         shQuote("alignment_files"), "must be equal.")
-        stopper(stp_msg)
+        len_peak_files <- if (is.list(peak_files)) length(peak_files) else 1
+        len_alignment_files <- if (is.list(alignment_files))
+            length(alignment_files) else 1
+        if (len_peak_files != len_alignment_files) {
+            stopper(stp_msg)
+        }
     }
     if (!is.null(cell_counts) && length(cell_counts) != length(peak_files)) {
         stp_msg <- paste0("Length of ", shQuote("cell_counts"), " must be ",
@@ -212,7 +216,12 @@ MotifPeeker <- function(
         paste0("MotifPeeker_", format(Sys.time(), "%Y%m%d_%H%M%S"))
         )
     dir.create(out_dir, showWarnings = debug)
+
+    ### Normalise input paths ###
     out_dir <- normalizePath(out_dir)
+    peak_files <- normalise_paths(peak_files)
+    alignment_files <- normalise_paths(alignment_files)
+    motif_files <- normalise_paths(motif_files)
 
     ### Store arguments in a list ###
     args_list <- list(

R/check_ENCODE.R

@@ -20,6 +20,7 @@
 #' 
 #' @export
 check_ENCODE <- function(encode_id, expect_format, verbose = FALSE) {
+    if (!all(is.character(encode_id))) return(encode_id)
     ### Validate ENCODE ID ###
     id_pattern <- "^ENC(SR|BS|DO|GM|AB|LB|FF|PL)\\d{3}[A-Z]{3}$"
     if (!all(grepl(id_pattern, encode_id))) return(encode_id)

R/normalise_paths.R

@@ -0,0 +1,23 @@
+#' Apply \code{\link[base]{normalizePath}} to a list of paths
+#' 
+#' @param path_list A list of paths.
+#' 
+#' @return A list of normalised paths or the input as is if contents are not
+#' a character.
+#' 
+#' @keywords internal
+normalise_paths <- function(path_list) {
+    if (all(is.null(path_list))) return(path_list)
+
+    ## Convert objects to list if not already
+    if (!is.list(path_list) &&(!is.vector(path_list) || length(path_list) == 1))
+        path_list <- list(path_list)
+
+    ## Return input as is if not character
+    if (!all(sapply(path_list, is.character))) return(path_list)
+
+    ## Normalise paths
+    lapply(path_list, function(path) {
+        normalizePath(path)
+    })
+}

inst/markdown/MotifPeeker.Rmd

@@ -80,20 +80,11 @@ result <- list(
     peaks = Vectorize(read_peak_file, "peak_file")(peak_files_encode),
     alignments = lapply(alignment_files_encode, Rsamtools::BamFile),
     exp_labels = params$exp_labels,
-    exp_type = unname(Vectorize(format_exptype,
-                        "exp_type")(exp_types))
+    exp_type = unname(Vectorize(format_exptype, "exp_type")(exp_types))
 )
-motif_files_jaspar <- if (motif_len > 1) {
-        Vectorize(check_JASPAR, "motif_id")(params$motif_files)
-    } else {
-        check_JASPAR(params$motif_files)
-    }
+motif_files_jaspar <- Vectorize(check_JASPAR, "motif_id")(params$motif_files)
 user_motifs <- list(
-    motifs = if (motif_len > 1) {
-            Vectorize(read_motif_file, "motif_file")(motif_files_jaspar)
-        } else if (motif_len == 1) {
-            read_motif_file(motif_files_jaspar)
-        },
+    motifs = Vectorize(read_motif_file, "motif_file")(motif_files_jaspar),
     motif_labels = params$motif_labels
 )
 result$alignments <- unname(result$alignments)
@@ -152,8 +143,6 @@ peak_width_df <-
                 peak_width = unlist(result$peak_widths))
 
 ## Motif-Summit Distances
-if (length(user_motifs$motifs) == 1) user_motifs$motifs <-
-    list(user_motifs$motifs)
 motif_summit_dist_df <- get_df_distances(
         result, user_motifs, genome_build, out_dir_extra, params$workers,
         params$meme_path, params$debug

tests/testthat/test-MotifPeeker.R

@@ -76,14 +76,17 @@ test_that("MotifPeeker produces output files", {
     expect_true(file.exists(file.path(out_dir, "MotifPeeker.html")))
 
     ## Single set of files
+    ## Also, try with built-in data
+    data("CTCF_ChIP_peaks", package = "MotifPeeker")
+    data("motif_MA1930.2", package = "MotifPeeker")
     out_dir <- MotifPeeker(
-      peak_files = peaks[1],
+      peak_files = CTCF_ChIP_peaks,
       reference_index = 1,
       alignment_files = alignments[1],
       exp_labels = c("ChIP"),
       exp_type = c("chipseq"),
       genome_build = "hg38",
-      motif_files = motifs[[1]],
+      motif_files = motif_MA1930.2,
       motif_labels = NULL,
       cell_counts = NULL,
       denovo_motif_discovery = TRUE,

tests/testthat/test-normalise_paths.R

@@ -0,0 +1,12 @@
+test_that("normalise_paths works", {
+    expect_null(normalise_paths(NULL))
+
+    ## Return non-character items as-is
+    data("CTCF_ChIP_peaks", package = "MotifPeeker")
+    expect_equal(normalise_paths(CTCF_ChIP_peaks)[[1]], CTCF_ChIP_peaks)
+
+    ## Return full paths from relative paths
+    file <- system.file("extdata", "CTCF_ChIP_alignment.bam",
+                        package = "MotifPeeker")
+    expect_equal(normalise_paths(file)[[1]], file)
+})