Plot tRNA secondary structure with modifications and linkages

Reads a bundled tRNA cloverleaf SVG and overlays modification highlights, outline circles, and circuit linkage arcs. Modifications are shown as colored filled circles behind nucleotide letters; outlines are shown as colored circle borders; linkages are drawn as Bezier curve arcs between position pairs.

Usage

plot_tRNA_structure(
  trna,
  organism,
  modifications = NULL,
  outlines = NULL,
  linkages = NULL,
  output = NULL,
  mod_palette = NULL,
  outline_palette = NULL,
  text_colors = NULL,
  position_markers = TRUE,
  linkage_palette = c("#0072B2", "#D55E00")
)

Arguments

trna

Character string identifying the tRNA (e.g., "tRNA-Ala-GGC"). Use structure_trnas() to list available tRNAs.

organism

Character string specifying the organism name (e.g., "Escherichia coli").

modifications

A tibble with columns pos (1-based position in the tRNA sequence) and mod1 (short modification name, e.g., "m1A"). Output of modomics_mods() works directly after filtering to the tRNA of interest.

outlines

A tibble with columns pos (1-based position) and group (category name for palette lookup). Draws circle outlines (stroke only, no fill) around each nucleotide.

linkages

A tibble with columns pos1, pos2, and optionally value (e.g., log odds ratio) for coloring arcs. If a log_odds_ratio column is present and value is not, it is automatically used as value, so output of clean_odds_ratios() or filter_linkages() works directly.

output

Path for the output SVG file. If NULL (default), writes to a temporary file.

mod_palette

Named character vector of colors keyed by modification short name. If NULL, uses a default palette.

outline_palette

Named character vector of colors keyed by outline group name. If NULL, uses "#333333" for all.

text_colors

A tibble with columns pos (1-based position) and color (hex color string). Changes the nucleotide letter color at specified positions. Unspecified positions keep the default color.

position_markers

Logical; if TRUE (default), draw small grey position numbers every 10 nucleotides around the cloverleaf to help orient readers.

linkage_palette

Character vector of length 2 giving the colors for negative (exclusive) and positive (co-occurring) linkage values. Default c("#0072B2", "#D55E00") (blue for exclusive, vermillion for co-occurring). Stroke width encodes the magnitude of the value.

Value

The path to the annotated SVG file (invisibly).

Examples

# \donttest{
plot_tRNA_structure("tRNA-Glu-TTC", "Escherichia coli")
# }