Refactor: remove dead code, relocate functions, migrate globals to .data$

- Remove unused interpolate_color() and first_child variable from plot-structure.R
- Move compute_ror() and compute_odds_ratios() to odds-ratios.R
- Move nucleotide_colors() and region_colors() to palettes.R
- Extract build_modomics_entries() helper to deduplicate modomics.R
- Fix roxygen tag ordering and add missing @examples
- Fix vignette cross-reference to rewiring article
- Fix pkgdown double-listing of plot functions
- Convert expect_error/expect_warning to expect_snapshot in tests
- Add tests for read_fasta, read_mod_annotations, compute_ror, read_pipeline_results
- Migrate all bare column names to .data$ pronoun or quoted strings
- Delete R/globals.R (162 lines of globalVariables no longer needed)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jayhesselberth

NAMESPACE

@@ -68,7 +68,6 @@ export(structure_trnas)
 export(tabulate_deseq)
 export(tidy_deseq_results)
 export(trna_regions)
-import(Biostrings)
 import(S4Vectors)
 import(SummarizedExperiment)
 import(ggplot2)

R/clover-se.R

@@ -110,31 +110,33 @@ create_clover <- function(
 
 #' Read FASTA reference
 #'
-#' @examples
-#' fa <- clover_example("ecoli/trna_only.fa.gz")
-#' read_fasta(fa)
-#'
-#' @param fa path to fasta file
+#' @param fa Path to a FASTA file.
 #'
 #' @return A [Biostrings::DNAStringSet].
-#' @import Biostrings
+#'
 #' @export
+#'
+#' @examples
+#' fa <- clover_example("ecoli/trna_only.fa.gz")
+#' read_fasta(fa)
 read_fasta <- function(fa) {
   Biostrings::readDNAStringSet(fa)
 }
 
 #' Read modifications file
 #'
-#' TSV file with 4 columns:
+#' Read a TSV file with 4 columns: `ref`, `pos`, `mod_full`, `mod1`.
 #'
-#' 1. `ref`
-#' 2. `pos`
-#' 3. `mod_full`
-#' 4. `mod1`
+#' @param mods Path to a modifications TSV file.
 #'
-#' @param mods path to modifications file
 #' @return A tibble.
+#'
 #' @export
+#'
+#' @examples
+#' \dontrun{
+#' read_mod_annotations("modifications.tsv")
+#' }
 read_mod_annotations <- function(mods) {
   readr::read_tsv(mods, show_col_types = FALSE)
 }

R/deseq.R

@@ -27,13 +27,13 @@ abundance_count_matrix <- function(charging_data, min_count = 10) {
   abundance <- charging_data |>
     dplyr::mutate(
       total_count = as.integer(
-        round(counts_charged + counts_uncharged)
+        round(.data$counts_charged + .data$counts_uncharged)
       )
     ) |>
-    dplyr::select(ref, sample_id, total_count) |>
+    dplyr::select("ref", "sample_id", "total_count") |>
     tidyr::pivot_wider(
-      names_from = sample_id,
-      values_from = total_count,
+      names_from = "sample_id",
+      values_from = "total_count",
       values_fill = 0L
     )
 
@@ -72,22 +72,22 @@ abundance_count_matrix <- function(charging_data, min_count = 10) {
 charging_count_matrix <- function(charging_data, min_count = 10) {
   long <- charging_data |>
     dplyr::mutate(
-      counts_charged = as.integer(round(counts_charged)),
-      counts_uncharged = as.integer(round(counts_uncharged))
+      counts_charged = as.integer(round(.data$counts_charged)),
+      counts_uncharged = as.integer(round(.data$counts_uncharged))
     ) |>
     tidyr::pivot_longer(
-      cols = c(counts_charged, counts_uncharged),
+      cols = dplyr::all_of(c("counts_charged", "counts_uncharged")),
       names_to = "charge_status",
       values_to = "count"
     ) |>
     dplyr::mutate(
-      charge_status = sub("^counts_", "", charge_status),
-      col_name = paste0(sample_id, "_", charge_status)
+      charge_status = sub("^counts_", "", .data$charge_status),
+      col_name = paste0(.data$sample_id, "_", .data$charge_status)
     ) |>
-    dplyr::select(ref, col_name, count) |>
+    dplyr::select("ref", "col_name", "count") |>
     tidyr::pivot_wider(
-      names_from = col_name,
-      values_from = count,
+      names_from = "col_name",
+      values_from = "count",
       values_fill = 0L
     )
 

R/globals.R

@@ -108,18 +108,18 @@ identity_elements <- function(
 
   result <- result |>
     dplyr::select(
-      amino_acid,
-      domain,
-      sprinzl_pos,
-      nucleotide,
-      region,
-      type,
-      strength,
-      pair_pos,
-      pair_type,
-      against_aars,
-      universal,
-      description
+      "amino_acid",
+      "domain",
+      "sprinzl_pos",
+      "nucleotide",
+      "region",
+      "type",
+      "strength",
+      "pair_pos",
+      "pair_type",
+      "against_aars",
+      "universal",
+      "description"
     )
 
   if (!is.null(amino_acid)) {
@@ -487,7 +487,7 @@ plot_identity_panel <- function(
 find_sprinzl_id <- function(trna, sprinzl_coords) {
   parts <- strsplit(trna, "-")[[1]]
   if (length(parts) >= 3) {
-    parts[3] <- gsub("T", "U", parts[3])
+    parts[3] <- chartr("T", "U", parts[3])
   }
   rna_name <- paste(parts, collapse = "-")
   pattern <- paste0("^nuc-", rna_name, "-")

R/identity.R

@@ -64,25 +64,7 @@ modomics_mods <- function(fasta, organism, min_identity = 0.7) {
     "Processing {nrow(modomics_seqs)} MODOMICS sequence{?s}."
   )
 
-  modomics_entries <- purrr::map(
-    seq_len(nrow(modomics_seqs)),
-    function(i) {
-      mods <- extract_mod_positions(
-        modomics_seqs$seq[i],
-        mod_dict
-      )
-      plain_seq <- strip_modifications(
-        modomics_seqs$seq[i],
-        mod_dict
-      )
-      list(
-        subtype = modomics_seqs$subtype[i],
-        anticodon = modomics_seqs$anticodon[i],
-        mods = mods,
-        plain_seq = plain_seq
-      )
-    }
-  )
+  modomics_entries <- build_modomics_entries(modomics_seqs, mod_dict)
 
   cli::cli_inform(
     "Matching MODOMICS sequences to reference FASTA."
@@ -123,6 +105,28 @@ modomics_organisms <- function() {
   gsub("_", " ", tools::file_path_sans_ext(rds_files))
 }
 
+build_modomics_entries <- function(modomics_seqs, mod_dict) {
+  purrr::map(
+    seq_len(nrow(modomics_seqs)),
+    function(i) {
+      mods <- extract_mod_positions(
+        modomics_seqs$seq[i],
+        mod_dict
+      )
+      plain_seq <- strip_modifications(
+        modomics_seqs$seq[i],
+        mod_dict
+      )
+      list(
+        subtype = modomics_seqs$subtype[i],
+        anticodon = modomics_seqs$anticodon[i],
+        mods = mods,
+        plain_seq = plain_seq
+      )
+    }
+  )
+}
+
 load_cached_modifications <- function() {
   path <- system.file(
     "extdata",
@@ -212,25 +216,7 @@ fetch_modomics_mods <- function(
     "Processing {nrow(modomics_seqs)} MODOMICS sequence{?s}."
   )
 
-  modomics_entries <- purrr::map(
-    seq_len(nrow(modomics_seqs)),
-    function(i) {
-      mods <- extract_mod_positions(
-        modomics_seqs$seq[i],
-        mod_dict
-      )
-      plain_seq <- strip_modifications(
-        modomics_seqs$seq[i],
-        mod_dict
-      )
-      list(
-        subtype = modomics_seqs$subtype[i],
-        anticodon = modomics_seqs$anticodon[i],
-        mods = mods,
-        plain_seq = plain_seq
-      )
-    }
-  )
+  modomics_entries <- build_modomics_entries(modomics_seqs, mod_dict)
 
   cli::cli_inform(
     "Matching MODOMICS sequences to reference FASTA."