Perl to r

.Rbuildignore

@@ -8,4 +8,5 @@
 ^R-deprecated$
 ^data-raw$
 ^pkgdown$
-^LICENSE.md$
+^LICENSE.md$
+^\.vscode$

.github/workflows/rhub.yaml

@@ -1,8 +1,8 @@
 # R-hub's generic GitHub Actions workflow file. It's canonical location is at
-# https://github.com/r-hub/rhub2/blob/v1/inst/workflow/rhub.yaml
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
 # You can update this file to a newer version using the rhub2 package:
 #
-# rhub2::rhub_setup()
+# rhub::rhub_setup()
 #
 # It is unlikely that you need to modify this file manually.
 
@@ -33,7 +33,7 @@ jobs:
 
     steps:
     # NO NEED TO CHECKOUT HERE
-    - uses: r-hub/rhub2/actions/rhub-setup@v1
+    - uses: r-hub/actions/setup@v1
       with:
         config: ${{ github.event.inputs.config }}
       id: rhub-setup
@@ -51,16 +51,16 @@ jobs:
       image: ${{ matrix.config.container }}
 
     steps:
-      - uses: r-hub/rhub2/actions/rhub-checkout@v1
-      - uses: r-hub/rhub2/actions/rhub-platform-info@v1
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/rhub2/actions/rhub-setup-deps@v1
+      - uses: r-hub/actions/setup-deps@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/rhub2/actions/rhub-run-check@v1
+      - uses: r-hub/actions/run-check@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
@@ -78,20 +78,20 @@ jobs:
     steps:
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-tinytex@v2
-      - uses: r-hub/rhub2/actions/rhub-checkout@v1
-      - uses: r-hub/rhub2/actions/rhub-setup-r@v1
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/rhub2/actions/rhub-platform-info@v1
+      - uses: r-hub/actions/platform-info@v1
         with:
           token: ${{ secrets.RHUB_TOKEN }}
           job-config: ${{ matrix.config.job-config }}
-      - uses: r-hub/rhub2/actions/rhub-setup-deps@v1
+      - uses: r-hub/actions/setup-deps@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}
-      - uses: r-hub/rhub2/actions/rhub-run-check@v1
+      - uses: r-hub/actions/run-check@v1
         with:
           job-config: ${{ matrix.config.job-config }}
           token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -10,3 +10,6 @@ vignettes-manual-export/
 /doc/
 /Meta/
 gggenomes.Rcheck
+.vscode
+gggenomes_*.tar.gz
+vignettes/gggenomes_cache

DESCRIPTION

@@ -6,17 +6,17 @@ Authors@R: c(
   person("Markus J.", "Ankenbrand", email = "[email protected]", role = c("aut")),
   person("Bart", "van Adrichem", role = c("aut")),
   person("Kristina", "Haslinger", email = "[email protected]", role = c("ctb", "sad")))
-Description: An extension of ggplot2 for creating complex genomic
- maps. It builds on the power of ggplot2 and tidyverse adding new ggplot-style
- geoms & positions and dplyr-style verbs to manipulate the underlying data. It
- implements a layout concept inspired by ggraph and introduces tracks to bring
- tidyness to the mess that is genomics data.
+Description: An extension of 'ggplot2' for creating complex genomic
+ maps. It builds on the power of 'ggplot2' and 'tidyverse' adding new 'ggplot2'-style
+ geoms & positions and 'dplyr'-style verbs to manipulate the underlying data. It
+ implements a layout concept inspired by 'ggraph' and introduces tracks to bring
+ tidiness to the mess that is genomics data.
 License: MIT + file LICENSE
 URL: https://github.com/thackl/gggenomes
 BugReports: https://github.com/thackl/gggenomes/issues
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr
 Depends:
@@ -43,7 +43,6 @@ Imports:
     ellipsis
 Suggests:
     testthat,
-    rtracklayer,
     ggtree,
     patchwork,
     Hmisc,

NAMESPACE

@@ -12,6 +12,8 @@ S3method(add_subfeats,gggenomes)
 S3method(add_subfeats,gggenomes_layout)
 S3method(add_sublinks,gggenomes)
 S3method(add_sublinks,gggenomes_layout)
+S3method(as_bounds,default)
+S3method(as_bounds,numeric)
 S3method(as_feats,default)
 S3method(as_feats,tbl_df)
 S3method(as_links,default)
@@ -73,6 +75,8 @@ S3method(track_ids,gggenomes)
 S3method(track_ids,gggenomes_layout)
 S3method(track_info,gggenomes)
 S3method(track_info,gggenomes_layout)
+S3method(tracks,gggenomes)
+S3method(tracks,gggenomes_layout)
 export("%<>%")
 export("%>%")
 export(GeomFeatText)
@@ -113,6 +117,7 @@ export(genes)
 export(geom_bin_label)
 export(geom_coverage)
 export(geom_feat)
+export(geom_feat_label)
 export(geom_feat_note)
 export(geom_feat_tag)
 export(geom_feat_text)
@@ -122,6 +127,7 @@ export(geom_gene_note)
 export(geom_gene_tag)
 export(geom_gene_text)
 export(geom_link)
+export(geom_link_label)
 export(geom_link_line)
 export(geom_seq)
 export(geom_seq_break)
@@ -160,6 +166,8 @@ export(qc)
 export(qw)
 export(read_alitv)
 export(read_bed)
+export(read_blast)
+export(read_context)
 export(read_fai)
 export(read_feats)
 export(read_gbk)
@@ -170,6 +178,7 @@ export(read_seq_len)
 export(read_seqs)
 export(read_subfeats)
 export(read_sublinks)
+export(read_vcf)
 export(require_vars)
 export(scale_color_variant)
 export(scale_shape_variant)
@@ -191,8 +200,12 @@ export(track)
 export(track_ids)
 export(track_info)
 export(unnest_exons)
+export(vars_track)
+export(width)
+export(width0)
 export(write_gff3)
 import(dplyr)
+import(ellipsis)
 import(ggplot2)
 import(grid)
 import(rlang)

R/aaa.R

@@ -6,18 +6,20 @@
 #' TRUE/FALSE vector
 #' @param ... the two columns bewteen which values are to be swapped in
 #' dplyr::select-like syntax
+#' @return a tibble with conditionally swapped start and end
 #' @examples
-#' x <- tibble::tibble(start = c(10,100), end=c(30, 50))
+#' x <- tibble::tibble(start = c(10, 100), end = c(30, 50))
 #' # ensure start of a range is always smaller than the end
 #' swap_if(x, start > end, start, end)
-swap_if <- function(x, condition, ...){
+swap_if <- function(x, condition, ...) {
   i <- tidyselect::eval_select(rlang::expr(c(...)), x)
-  if(length(i) != 2 || length(unique(i)) != 2)
+  if (length(i) != 2 || length(unique(i)) != 2) {
     rlang::abort("need to select exactly 2 different columns for swapping")
+  }
   # eval condition in data context
-  j <- transmute(x, j = {{condition}})$j
+  j <- transmute(x, j = {{ condition }})$j
   # swap
-  x[j,rev(i)] <- x[j,i]
+  x[j, rev(i)] <- x[j, i]
   x
 }
 
@@ -26,13 +28,15 @@ swap_if <- function(x, condition, ...){
 #' @param x vector (coerced to character)
 #' @param collapse character string to separate elements.
 #' @keywords internal
-comma <- function(x, collapse = ","){
-    paste(x, collapse=collapse)
+#' @noRd
+comma <- function(x, collapse = ",") {
+  paste(x, collapse = collapse)
 }
 
 #' Get path to gggenomes example files
 #' @export
 #' @param file name of example file
+#' @return path to example file
 ex <- function(file = NULL) {
   if (is.null(file)) {
     dir(system.file("extdata", package = "gggenomes"))
@@ -42,21 +46,23 @@ ex <- function(file = NULL) {
 }
 
 # are there any arguments in ...
-has_dots <- function(env = parent.frame()){
+has_dots <- function(env = parent.frame()) {
   length(ellipsis__dots(env)) > 0
 }
 
-shared_names <- function(x, ...){
+shared_names <- function(x, ...) {
   names <- c(...)
   names[names %in% names2(x)]
 }
 
 # split a vector of tuples c(a1,b2,a2,b2) into a list of two vectors
 # list(a=c(a1,a2), b=c(b1,b2))
-vec_unzip <- function(x, names=NULL, ignore_odd=FALSE){
-  if(!ignore_odd && length(x)%%2){
-    abort(str_glue("Won't unzip a vector of uneven length {(length(x))}\n",
-                   "Disable error with `ignore_odd=TRUE`"))
+vec_unzip <- function(x, names = NULL, ignore_odd = FALSE) {
+  if (!ignore_odd && length(x) %% 2) {
+    abort(str_glue(
+      "Won't unzip a vector of uneven length {(length(x))}\n",
+      "Disable error with `ignore_odd=TRUE`"
+    ))
   }
 
   i <- c(TRUE, FALSE)
@@ -79,14 +85,15 @@ magrittr::`%<>%`
 #'
 #' @export
 #' @param key variable to split by
+#' @return a list of tibbles
 #' @keywords internal
 #' @examples
-#' tibble::tibble(x=c(1,1,1,2), y=c("B", "A", "B", "B"), z="foo") %>%
+#' tibble::tibble(x = c(1, 1, 1, 2), y = c("B", "A", "B", "B"), z = "foo") %>%
 #'   split_by(x)
-split_by <- function(.data, key){
+split_by <- function(.data, key) {
   keys <- pull(.data, !!enquo(key))
 
-  if(length(keys) == 0) stop("no keys to index by found\n")
+  if (length(keys) == 0) stop("no keys to index by found\n")
 
   l <- split(.data, keys)
   l[unique(keys)]
@@ -101,7 +108,7 @@ split_by <- function(.data, key){
 #' Took inspiration from
 #' \href{https://stackoverflow.com/questions/520810/does-r-have-quote-like-operators-like-perls-qw}{stackoverflow/qw}
 #' and \href{https://github.com/jebyrnes/multifunc/blob/master/R/qw.R}{github/Jarrett Byrnes}
-#' 
+#'
 #' @export
 #' @param x A single string of elements to be split at whitespace chars.
 #' @return A vector of quoted words.
@@ -120,10 +127,18 @@ qc <- function(...) sapply(match.call()[-1], deparse)
 # CRAN Workaround for unexported useful tidyverse internals
 # https://stackoverflow.com/questions/32535773/using-un-exported-function-from-another-r-package
 ggplot2__ggname <- utils::getFromNamespace("ggname", "ggplot2")
-ggplot2__rd_aesthetics <- utils::getFromNamespace("rd_aesthetics", "ggplot2")
+ggplot2__rd_aesthetics <- \(x, y) utils::getFromNamespace("rd_aesthetics", "ggplot2")(x, y) |> stringr::str_replace(stringr::fixed("link[="), "link[ggplot2:")
 ggplot2__scales_list <- utils::getFromNamespace("scales_list", "ggplot2")
 ggplot2__guides_list <- utils::getFromNamespace("guides_list", "ggplot2")
 ggplot2__make_labels <- utils::getFromNamespace("make_labels", "ggplot2")
 ellipsis__dots <- utils::getFromNamespace("dots", "ellipsis")
 scales__force_all <- utils::getFromNamespace("force_all", "scales")
 purrr__as_mapper.default <- utils::getFromNamespace("as_mapper.default", "purrr")
+
+# Additional fix for seamingly unused package in imports due to the workaround above
+# https://forum.posit.co/t/new-r-cmd-check-note-in-r-4-2-0-for-imports-field/143153/4
+#' @import ellipsis
+#' @noRd
+dummy <- function() {
+  ellipsis::safe_median
+}

R/add_tracks.R

@@ -1,5 +1,5 @@
 #' Add different types of tracks
-#' 
+#'
 #' @name add_tracks
 #' @param x object to add the tracks to (e.g. gggenomes, gggenomes_layout)
 #' @param ... named data.frames, i.e. genes=gene_df, snps=snp_df

R/aes.R

@@ -1,23 +1,24 @@
 # thomasp85/ggraph https://github.com/thomasp85/ggraph/blob/master/R/aaa.R
 aes_intersect <- function(aes1, aes2) {
-    structure(
-        c(as.list(aes1), aes2[!names(aes2) %in% names(aes1)]),
-        class = 'uneval'
-    )
+  structure(
+    c(as.list(aes1), aes2[!names(aes2) %in% names(aes1)]),
+    class = "uneval"
+  )
 }
 
-aes_nudge_by_strand <- function(mapping, nudge_by_strand, keys = c("y", "yend")){
-  if(is.null(nudge_by_strand))
+aes_nudge_by_strand <- function(mapping, nudge_by_strand, keys = c("y", "yend")) {
+  if (is.null(nudge_by_strand)) {
     return(mapping)
+  }
 
   # modify y/yend aes
   is_integer(nudge_by_strand) || is_double(nudge_by_strand) ||
     stop("nudge_by_strand needs to be numeric")
 
-  for(k in keys){
-    if(is.null(mapping[[k]])) stop("'", k, "' not defined, cannot modify")
+  for (k in keys) {
+    if (is.null(mapping[[k]])) stop("'", k, "' not defined, cannot modify")
 
-    mapping[[k]] <- rlang::parse_expr(paste0(rlang::quo_text(mapping[[k]]),'+ display_strand * ',-nudge_by_strand))
+    mapping[[k]] <- rlang::parse_expr(paste0(rlang::quo_text(mapping[[k]]), "+ display_strand * ", -nudge_by_strand))
   }
   mapping
 }