Plot tRNA structure with identity element overlays — plot_identity

Generates a tRNA cloverleaf structure SVG with aminoacylation identity elements highlighted as colored outlines. Strong determinants are shown in red, weak determinants in blue.

Usage

plot_identity_structure(
  trna,
  organism,
  sprinzl_coords,
  trna_id = NULL,
  amino_acid = NULL,
  outline_palette = NULL,
  ...
)

Arguments

trna: Character string identifying the tRNA (e.g., "tRNA-Ala-AGC"). Use structure_trnas() to list available tRNAs.
organism: Character string specifying the organism name (e.g., "Saccharomyces cerevisiae").
sprinzl_coords: A tibble of Sprinzl coordinates as returned by read_sprinzl_coords().
trna_id: Character string identifying the tRNA in sprinzl_coords (e.g., "nuc-tRNA-Ala-AGC-1-1"). If NULL (default), auto-detected from trna by converting the anticodon to RNA (T to U) and matching the first Sprinzl entry.
amino_acid: Optional 3-letter amino acid code. If NULL (default), extracted from the trna name.
outline_palette: Named character vector of colors keyed by strength ("strong", "weak"). Default uses red for strong and blue for weak determinants.
...: Additional arguments passed to plot_tRNA_structure().

Value

The path to the annotated SVG file (invisibly).

Examples

# \donttest{
coords <- read_sprinzl_coords(
  clover_example("sprinzl/sacCer_global_coords.tsv.gz")
)
plot_identity_structure(
  "tRNA-Ala-AGC", "Saccharomyces cerevisiae", coords
)
# }