plot_tRNA_structure() silently draws overlapping circles for duplicate positions

[jayhesselberth]

Problem

When plot_tRNA_structure() receives a modifications tibble with duplicate positions (e.g., a position that is both a MODOMICS modification and part of a user-added "anticodon" group via bind_rows()), two semi-transparent filled circles are drawn at the same coordinates. The colors blend unpredictably due to fill-opacity = "0.6", and the legend shows both entries as if they are distinct.

There is no deduplication, warning, or error — the collision is silent.

Reproduction

The vignette pattern of combining MODOMICS modifications with a user-defined anticodon group triggers this when an anticodon position (e.g., Sprinzl 34) also has a MODOMICS modification:

mods <- get_modifications(clov)
anticodon <- tibble(pos = 34:36, mod1 = "anticodon")
combined <- bind_rows(mods, anticodon)

# Position 34 now appears twice — once as a MODOMICS mod, once as "anticodon"
plot_tRNA_structure(combined)

Affected code

add_mod_circles() in R/plot-structure.R:390-413 iterates all rows without checking for duplicate positions:

for (i in seq_len(nrow(modifications))) {
    mod_pos <- modifications$pos[i]
    # ...
    xml2::xml_add_child(
      mod_group,
      "circle",
      cx = as.character(nuc$x + nuc_x_offset),
      cy = as.character(nuc$y + nuc_y_offset),
      r = "4.3",
      fill = color,
      "fill-opacity" = "0.6",
      stroke = "none"
    )
}

Suggestion

Deduplicate by position before drawing circles (last entry wins, matching bind_rows() semantics), and emit a cli::cli_warn() listing the affected positions so users know their data had collisions.