diff --git a/NEWS.md b/NEWS.md index d4cfa50..f7c1396 100644 --- a/NEWS.md +++ b/NEWS.md @@ -28,6 +28,8 @@ * `filter_linkages()` filters odds ratio data by p-value, observation count, and log odds ratio magnitude, returning a tibble ready for the `linkages` parameter of `plot_tRNA_structure()`. +* `plot_tRNA_structure()` gains a `layout` argument with `"cloverleaf"` (default) and `"elbow"` forms; the elbow form stacks the acceptor stem and T-arm coaxially at the top with the D-arm extending horizontally and the anticodon arm vertically. Currently bundled for E. coli standard 3-arm tRNAs. `structure_trnas()` accepts the same `layout` argument. + * `plot_tRNA_structure()` now accepts odds ratio tibbles directly as `linkages` input: if a `log_odds_ratio` column is present and `value` is not, it is automatically used as the arc value. * `plot_tRNA_structure()` now draws a 3' amino acid label (e.g., "Glu") connected by a line to the terminal nucleotide, and position markers every 10 nucleotides around the cloverleaf. Position markers can be disabled with `position_markers = FALSE`. diff --git a/R/plot-structure.R b/R/plot-structure.R index a257a2a..756343e 100644 --- a/R/plot-structure.R +++ b/R/plot-structure.R @@ -27,12 +27,14 @@ structure_organisms <- function() { #' List available tRNA structures for an organism #' -#' Returns the names of tRNAs for which cloverleaf structure SVGs -#' are bundled with the package for the given organism. +#' Returns the names of tRNAs for which structure SVGs are bundled with +#' the package for the given organism and layout. #' #' @param organism Character string specifying the organism name #' (e.g., `"Escherichia coli"`). Use [structure_organisms()] to #' list available organisms. +#' @param layout One of `"cloverleaf"` (default) or `"elbow"`. The +#' elbow form is currently bundled for E. coli standard tRNAs only. #' #' @return A character vector of tRNA names. #' @@ -40,9 +42,19 @@ structure_organisms <- function() { #' #' @examples #' structure_trnas("Escherichia coli") -structure_trnas <- function(organism) { +#' structure_trnas("Escherichia coli", layout = "elbow") +structure_trnas <- function(organism, layout = c("cloverleaf", "elbow")) { + layout <- match.arg(layout) org_dir <- structure_org_dir(organism) - svg_files <- list.files(org_dir, pattern = "\\.svg$") + svg_dir <- if (layout == "cloverleaf") { + org_dir + } else { + file.path(org_dir, "elbow") + } + if (!dir.exists(svg_dir)) { + return(character(0)) + } + svg_files <- list.files(svg_dir, pattern = "\\.svg$") tools::file_path_sans_ext(svg_files) } @@ -89,6 +101,12 @@ structure_trnas <- function(organism) { #' linkage values. Default `c("#0072B2", "#D55E00")` (blue for #' exclusive, vermillion for co-occurring). Stroke width encodes #' the magnitude of the value. +#' @param layout One of `"cloverleaf"` (default) or `"elbow"`. +#' `"elbow"` renders the L-shaped depiction with the acceptor stem +#' and T-arm stacked coaxially at the top, the D-arm extending +#' horizontally, and the anticodon arm hanging vertically. The +#' elbow form is currently available for E. coli standard +#' 3-arm tRNAs. #' #' @return The path to the annotated SVG file (invisibly). #' @@ -97,6 +115,7 @@ structure_trnas <- function(organism) { #' @examples #' \donttest{ #' plot_tRNA_structure("tRNA-Glu-TTC", "Escherichia coli") +#' plot_tRNA_structure("tRNA-Phe-GAA", "Escherichia coli", layout = "elbow") #' } plot_tRNA_structure <- function( trna, @@ -109,24 +128,31 @@ plot_tRNA_structure <- function( outline_palette = NULL, text_colors = NULL, position_markers = TRUE, - linkage_palette = c("#0072B2", "#D55E00") + linkage_palette = c("#0072B2", "#D55E00"), + layout = c("cloverleaf", "elbow") ) { rlang::check_installed("jsonlite", reason = "to read structure metadata.") + layout <- match.arg(layout) org_dir <- structure_org_dir(organism) + layout_dir <- if (layout == "cloverleaf") { + org_dir + } else { + file.path(org_dir, "elbow") + } - svg_path <- file.path(org_dir, paste0(trna, ".svg")) - json_path <- file.path(org_dir, paste0(trna, ".json")) + svg_path <- file.path(layout_dir, paste0(trna, ".svg")) + json_path <- file.path(layout_dir, paste0(trna, ".json")) if (!file.exists(svg_path)) { cli::cli_abort(c( - "No structure SVG found for {.val {trna}}.", - "i" = "Use {.fn structure_trnas} to list available tRNAs." + "No {layout} structure SVG found for {.val {trna}}.", + "i" = "Use {.code structure_trnas({.val {organism}}, layout = {.val {layout}})} to list available tRNAs." )) } if (!file.exists(json_path)) { cli::cli_abort( - "No position metadata found for {.val {trna}}." + "No position metadata found for {.val {trna}} in {layout} layout." ) } diff --git a/data-raw/structures/generate_elbow.py b/data-raw/structures/generate_elbow.py new file mode 100644 index 0000000..688c781 --- /dev/null +++ b/data-raw/structures/generate_elbow.py @@ -0,0 +1,557 @@ +"""Generate tRNA elbow-form SVGs from existing cloverleaf JSON metadata. + +Reads each E. coli tRNA's existing JSON (for sequence) and the Sprinzl +coordinates TSV (for per-position canonical Sprinzl labels), then emits an +elbow-form SVG and JSON in the SAME schema as the cloverleaf path. The +R-side overlay code in plot_tRNA_structure() consumes both layouts +identically. + +The elbow form (per Matsumoto et al., JBC 2026; see also classical +structural-biology depictions) lays out the molecule so that the acceptor +stem and T-arm are stacked coaxially as one horizontal helix at the top, +the D-arm extends horizontally to the left below it, the anticodon arm +hangs vertically below, and the variable region forms a small bulge +between the AC-stem and T-stem. + +Skips variable-arm tRNAs (Leu, Ser, SeC, Tyr, some Thr) — those will need +a v2 layout that handles the variable arm. + +Usage +----- + pixi run -e struct python data-raw/structures/generate_elbow.py +""" + +from __future__ import annotations + +import csv +import gzip +import json +import math +import re +import sys +from pathlib import Path + +# --- paths -------------------------------------------------------------- + +PROJECT_ROOT = Path(__file__).resolve().parent.parent.parent +SCRIPT_DIR = Path(__file__).resolve().parent +STRUCTURES_DIR = PROJECT_ROOT / "inst" / "extdata" / "structures" +SPRINZL_DIR = PROJECT_ROOT / "inst" / "extdata" / "sprinzl" + +# Map organism dir name -> Sprinzl coords filename +ORG_SPRINZL = { + "Escherichia_coli": "ecoliK12_global_coords.tsv.gz", +} + +# --- layout constants --------------------------------------------------- + +S = 7.56 # backbone spacing along a strand +P = 7.56 # vertical pair spacing between rows of a stem + +# Combined acceptor + T helix at top +TOP_Y = 40.0 # 3' strand row (acceptor 3' + T-stem 3'); CCA emerges UP from here +BOT_Y = TOP_Y + P # 5' strand row (acceptor 5' + T-stem 5'); side arms emerge DOWN from here +ACC_X1 = 220.0 # x of pos 1 (5' free end) and pos 72 (paired with pos 1) +GAP = S * 1.6 # break between T-stem and acceptor on the bottom strand + +# T-loop (54..60) curls at far LEFT of the combined helix. With N residues +# placed on a 180° arc at t = (k+0.5)/N, neighbors are 2R*sin(π/(2N)) apart. +# Solve for R so chord = S → R = S / (2 sin(π/(2N))). Matches the cloverleaf +# spacing so mod circles (radius 4.3) fit cleanly. +T_LOOP_RADIUS = S / (2 * math.sin(math.pi / 14)) # 7 residues + +# Both D-arm and AC-arm hang DOWN as parallel vertical helices below the top +# stack — D-arm to the LEFT (smaller, 4 bp + D-loop at the bottom-left), +# AC-arm to the RIGHT (larger, 5 bp + AC-loop at the bottom). Together with +# the horizontal acceptor+T helix at the top this gives the canonical L-shape +# elbow projection seen in textbook tRNA depictions (e.g., Matsumoto 2026 +# JBC fig 2A). +# +# Spacing is generous enough that the radius-4.3 modification circles and +# radius ~5 outline circles used by plot_tRNA_structure() do not collide +# with neighboring nucleotide letters. +D_X_LEFT = 130.0 # left column of D-stem (pos 10-13) +D_X_RIGHT = D_X_LEFT + P +D_TOP_Y = BOT_Y + 50.0 +D_LOOP_RADIUS = S / (2 * math.sin(math.pi / 16)) # 8 residues on 180° arc + +AC_X_LEFT = 158.0 +AC_X_RIGHT = AC_X_LEFT + P +AC_TOP_Y = D_TOP_Y # AC-arm aligned vertically with D-arm +AC_LOOP_RADIUS = S / (2 * math.sin(math.pi / 14)) # 7 residues on 180° arc + +# --- variable-arm detection -------------------------------------------- + +# A sprinzl label like "e1", "e12", "e23" indicates a variable-arm position; +# these tRNAs (Leu, Ser, SeC, some Tyr/Thr) have an extended variable arm +# that the v1 elbow layout does not handle. Skip them. +VAR_ARM_RE = re.compile(r"^e\d") + + +def main() -> int: + total_written = 0 + total_skipped = 0 + + for org_dirname, sprinzl_fname in ORG_SPRINZL.items(): + org_dir = STRUCTURES_DIR / org_dirname + if not org_dir.is_dir(): + print(f" SKIP {org_dirname}: structures dir not found") + continue + + sprinzl_path = SPRINZL_DIR / sprinzl_fname + if not sprinzl_path.exists(): + print(f" SKIP {org_dirname}: sprinzl file not found at {sprinzl_path}") + continue + + print(f"\n=== {org_dirname} ===") + sprinzl = load_sprinzl(sprinzl_path) + out_dir = org_dir / "elbow" + out_dir.mkdir(parents=True, exist_ok=True) + + # Clean stale output + for old in out_dir.glob("*.svg"): + old.unlink() + for old in out_dir.glob("*.json"): + old.unlink() + + for json_path in sorted(org_dir.glob("*.json")): + trna_name = json_path.stem + try: + metadata = json.loads(json_path.read_text()) + except Exception as e: + print(f" ERROR reading {trna_name}: {e}") + continue + + sprinzl_rows = lookup_sprinzl(sprinzl, trna_name) + if sprinzl_rows is None: + print(f" SKIP {trna_name}: no Sprinzl mapping found") + total_skipped += 1 + continue + + if any(VAR_ARM_RE.match(r["sprinzl_label"]) for r in sprinzl_rows): + print(f" SKIP {trna_name}: variable-arm tRNA (deferred to v2)") + total_skipped += 1 + continue + + try: + elbow_meta = build_elbow(metadata, sprinzl_rows, trna_name) + except KeyError as e: + print(f" SKIP {trna_name}: missing layout key {e}") + total_skipped += 1 + continue + + svg_path = out_dir / f"{trna_name}.svg" + elbow_json_path = out_dir / f"{trna_name}.json" + svg_path.write_text(render_svg(elbow_meta, trna_name)) + elbow_json_path.write_text(json.dumps(elbow_meta, indent=2)) + n = len(elbow_meta["nucleotides"]) + print(f" OK {trna_name} ({n} nt)") + total_written += 1 + + print(f"\nWrote {total_written} elbow tRNA(s); skipped {total_skipped}.") + return 0 + + +# --- Sprinzl loading + lookup ------------------------------------------ + + +def load_sprinzl(path: Path) -> dict[str, list[dict]]: + """Group Sprinzl rows by trna_id.""" + by_id: dict[str, list[dict]] = {} + with gzip.open(path, "rt") as f: + reader = csv.DictReader(f, delimiter="\t") + for row in reader: + tid = row["trna_id"] + try: + row["seq_index"] = int(row["seq_index"]) + except (KeyError, ValueError): + continue + by_id.setdefault(tid, []).append(row) + return by_id + + +def lookup_sprinzl( + sprinzl: dict[str, list[dict]], trna_name: str +) -> list[dict] | None: + """Find a Sprinzl row block whose trna_id matches the structure name. + + Structure names use DNA anticodon notation (e.g., 'tRNA-Asp-GTC') while + Sprinzl files use RNA notation ('tRNA-Asp-GUC'). Convert T→U in the + anticodon segment before matching. + """ + rna_name = dna_to_rna_anticodon(trna_name) + + candidates = [ + tid for tid in sprinzl + if tid == rna_name or tid.startswith(rna_name + "-") + ] + if not candidates: + return None + candidates.sort() + rows = sprinzl[candidates[0]] + rows.sort(key=lambda r: r["seq_index"]) + return rows + + +def dna_to_rna_anticodon(trna_name: str) -> str: + m = re.match(r"^(tRNA-[A-Za-z0-9]+)-([ACGTU]+)$", trna_name) + if not m: + return trna_name + aa, codon = m.group(1), m.group(2) + return f"{aa}-{codon.replace('T', 'U')}" + + +# --- elbow geometry ----------------------------------------------------- + + +def build_elbow( + cloverleaf_meta: dict, sprinzl_rows: list[dict], trna_name: str +) -> dict: + """Compute elbow (x, y) for each nucleotide from its Sprinzl label. + + The cloverleaf metadata gives us the per-position bases and base-pair + line list (which we recompute against the new coords). The Sprinzl + rows give us the Sprinzl label and region per position. We index + nucleotides in the cloverleaf JSON by `pos` (1-based, document order) + and join to Sprinzl rows by `seq_index`. + """ + base_by_pos = {nuc["pos"]: nuc["base"] for nuc in cloverleaf_meta["nucleotides"]} + sprinzl_by_pos = {r["seq_index"]: r for r in sprinzl_rows} + + coord_table = elbow_coord_table() + + nucleotides = [] + pos_to_xy: dict[int, tuple[float, float]] = {} + for pos in sorted(base_by_pos.keys()): + spr = sprinzl_by_pos.get(pos) + if spr is None: + raise KeyError(f"pos {pos} missing from Sprinzl rows") + label = spr["sprinzl_label"] + if label not in coord_table: + raise KeyError(f"label {label!r} (pos {pos})") + x, y = coord_table[label] + pos_to_xy[pos] = (x, y) + nucleotides.append({ + "base": base_by_pos[pos], + "x": round(x, 2), + "y": round(y, 2), + "pos": pos, + }) + + lines = build_pair_lines(sprinzl_by_pos, pos_to_xy) + + xs = [n["x"] for n in nucleotides] + ys = [n["y"] for n in nucleotides] + width = round(max(xs) + 20, 2) + height = round(max(ys) + 20, 2) + + return { + "nucleotides": nucleotides, + "width": width, + "height": height, + "lines": lines, + "trna_name": trna_name, + "sequence": cloverleaf_meta.get("sequence", ""), + "structure": cloverleaf_meta.get("structure", ""), + } + + +def elbow_coord_table() -> dict[str, tuple[float, float]]: + """Sprinzl label -> (x, y) for the elbow layout. + + Top combined helix: + Top row (3' strand, continuous backbone L->R): + 61 62 63 64 65 66 67 68 69 70 71 72 + Bottom row (5' strand, with gap between T-stem and acceptor): + 53 52 51 50 49 [GAP] 7 6 5 4 3 2 1 + Pair vertically: 1<->72, 2<->71, ... 7<->66; 49<->65, 50<->64, ... 53<->61. + + T-loop (54..60) curls at far LEFT of the combined helix. + D-arm sits BELOW the top stack, horizontal, with D-loop at far LEFT. + AC-arm hangs DOWN below the rest, with AC-loop at the BOTTOM. + Variable region (44..48) curves from the right of the AC-stem 3' end + UP and OVER to position 49 on the top stack. + Discriminator + CCA (73..76) extend UP from pos 72 (top-right). + """ + coords: dict[str, tuple[float, float]] = {} + + # ----- acceptor stem (1..7 bottom row, 66..72 top row) ----- + for n in range(1, 8): + x = ACC_X1 - (n - 1) * S + coords[str(n)] = (x, BOT_Y) + for n in range(66, 73): + x = ACC_X1 - (72 - n) * S + coords[str(n)] = (x, TOP_Y) + + # rightmost / leftmost x of acceptor section + acc_left_x = ACC_X1 - 6 * S # x of pos 7 / pos 66 + t_right_x = acc_left_x - GAP # x of pos 49 / pos 65 (across the gap) + + # ----- T-stem (49..53 bottom row, 61..65 top row) ----- + for n in range(49, 54): + x = t_right_x - (n - 49) * S + coords[str(n)] = (x, BOT_Y) + for n in range(61, 66): + x = t_right_x - (65 - n) * S + coords[str(n)] = (x, TOP_Y) + + t_left_x = t_right_x - 4 * S # x of pos 53 / pos 61 + + # ----- T-loop (54..60), 7 residues on a 180° arc curling LEFT ----- + arc_cx = t_left_x - T_LOOP_RADIUS * 0.35 + arc_cy = (TOP_Y + BOT_Y) / 2 + for k, n in enumerate(range(54, 61)): + # k = 0..6, sweep from "just past pos 53" (bottom) up & around to + # "just before pos 61" (top). In SVG y-down: angle pi/2 = down, + # angle 3pi/2 = up; sweeping through pi (left). + t = (k + 0.5) / 7 # 1/14, 3/14, ..., 13/14 + theta = math.pi / 2 + t * math.pi + x = arc_cx + T_LOOP_RADIUS * math.cos(theta) + y = arc_cy + T_LOOP_RADIUS * math.sin(theta) + coords[str(n)] = (x, y) + + # ----- discriminator + CCA (73..76) extend UP from pos 72 ----- + cca_x = ACC_X1 + for k, n in enumerate(range(73, 77)): + # 73 just above 72 on the same column, 74-76 stacking up + coords[str(n)] = (cca_x, TOP_Y - (k + 1) * S) + + # ----- D-arm: VERTICAL stem, D-loop curls at BOTTOM-LEFT ----- + # pos 10 (D-stem 5' first) at TOP-LEFT — paired with pos 25 at TOP-RIGHT. + # Stem extends DOWN from there; pos 13 at BOTTOM-LEFT, pos 22 at BOTTOM- + # RIGHT. D-loop (14..21) is a 180° arc connecting pos 13 (bottom-left) + # around the LEFT side back up to pos 22 (bottom-right) — i.e., it + # bulges LEFT and DOWN from the bottom of the stem, matching the + # canonical L-shape projection. + # Hinges 8, 9 are the diagonal connector from pos 7 (top stack, bot row, + # at acc_left_x) DOWN-LEFT to pos 10 (top-left of D-arm). Place evenly + # along the line so consecutive backbone neighbors are similarly spaced. + for k, n in enumerate(("8", "9"), start=1): + t = k / 3.0 # 1/3 and 2/3 along the line from pos 7 to pos 10 + coords[n] = ( + acc_left_x + (D_X_LEFT - acc_left_x) * t, + BOT_Y + (D_TOP_Y - BOT_Y) * t, + ) + # D-stem 5' (10..13) on LEFT column, top-to-bottom + for n in range(10, 14): + coords[str(n)] = (D_X_LEFT, D_TOP_Y + (n - 10) * S) + # D-stem 3' (22..25) on RIGHT column; pair: 25-10, 24-11, 23-12, 22-13 + for n in range(22, 26): + coords[str(n)] = (D_X_RIGHT, D_TOP_Y + (25 - n) * S) + + d_bot_y = D_TOP_Y + 3 * S # y of pos 13 / pos 22 + + # ----- D-loop (14..21), 8 residues on a 180° arc curling LEFT-and-DOWN ----- + # Arc center sits a bit DOWN-LEFT of the stem bottom. Sweep angle covers + # the LEFT half of the circle, from "just past pos 13" (top of arc, bot + # of stem on left col) curving DOWN through far-LEFT and back UP to + # "just before pos 22" (top of arc, bot of stem on right col). + arc_cx_d = D_X_LEFT + P / 2 + arc_cy_d = d_bot_y + D_LOOP_RADIUS * 0.55 + for k, n in enumerate(range(14, 22)): + t = (k + 0.5) / 8 + # Parameterize: angle from pi (left of stem-left-column-bottom) + # sweeping CCW through 3pi/2 (BOTTOM of arc) to 2pi (right side). + # In SVG y-down, y = cy + r*sin(theta) — sin pi to 2pi gives 0 to 0 + # via -1 at 3pi/2; we want POSITIVE y at the bottom of the arc, so + # use abs offset. + theta = math.pi + t * math.pi + x = arc_cx_d + D_LOOP_RADIUS * math.cos(theta) + y = arc_cy_d - D_LOOP_RADIUS * math.sin(theta) + coords[str(n)] = (x, y) + + # D-loop insertions: 17a is between 17 and 18; 20a between 20 and 21; + # 20b between 20a and 21. Place them on the same arc with offset t. + insertion_ts = { + "17a": (3.5 + 0.5) / 8, + "20a": (6.3 + 0.5) / 8, + "20b": (6.6 + 0.5) / 8, + } + for label, t in insertion_ts.items(): + theta = math.pi + t * math.pi + x = arc_cx_d + D_LOOP_RADIUS * math.cos(theta) + y = arc_cy_d - D_LOOP_RADIUS * math.sin(theta) + coords[label] = (x, y) + + # ----- pos 26 (hinge between D-stem 3' top and AC-stem 5' top) ----- + # short horizontal bridge from D-arm TOP-RIGHT (pos 25) over to AC-arm + # TOP-LEFT (pos 27). Both at the same y as the top of the side arms. + coords["26"] = ( + (D_X_RIGHT + AC_X_LEFT) / 2, + D_TOP_Y - 2.5, + ) + + # ----- anticodon stem (27..31 left col, 39..43 right col) ----- + # VERTICAL helix to the RIGHT of the D-arm. Pairs: 27-43, 28-42, ..., 31-39 + # 27 at top-left, 31 at bottom-left (just above AC-loop). + for n in range(27, 32): + y = AC_TOP_Y + (n - 27) * S + coords[str(n)] = (AC_X_LEFT, y) + for n in range(39, 44): + y = AC_TOP_Y + (43 - n) * S + coords[str(n)] = (AC_X_RIGHT, y) + + ac_bot_y = AC_TOP_Y + 4 * S # y of pos 31 / pos 39 + + # ----- AC-loop (32..38), 7 residues on 180° arc curling DOWN ----- + arc_cx_ac = (AC_X_LEFT + AC_X_RIGHT) / 2 + arc_cy_ac = ac_bot_y + AC_LOOP_RADIUS * 0.35 + for k, n in enumerate(range(32, 39)): + t = (k + 0.5) / 7 + # sweep from angle pi (left, near pos 31 column) to 0 (right, near pos 39 column) + # going DOWN through 3pi/2 (in y-down convention, that's bottom). + # parameterize: theta = pi - t * pi (pi to 0) + # but we want the arc to bulge DOWNWARD (positive y in SVG) + theta = math.pi - t * math.pi + x = arc_cx_ac + AC_LOOP_RADIUS * math.cos(theta) + # bulge down: use abs(sin) so all loop residues have y > arc_cy_ac + y = arc_cy_ac + AC_LOOP_RADIUS * abs(math.sin(theta)) + coords[str(n)] = (x, y) + + # ----- variable region (44..48): smooth curve from AC-stem 3' top to pos 49 ----- + # The bulge runs from pos 43 (top-right of AC-stem) up to pos 49 (T-stem + # 5' end on bottom row of top stack). Quadratic bezier with control + # point bowed RIGHT so the path doesn't crowd the AC-stem 3' column. + # Positions are placed by ARC-LENGTH along the curve so consecutive + # neighbors are evenly spaced (a t-uniform sampling clusters at the apex). + var_start = (AC_X_RIGHT, AC_TOP_Y - 0.6 * S) + var_end = (t_right_x + 0.3 * S, BOT_Y + 0.6 * S) + ctrl_x = max(var_start[0], var_end[0]) + 18 + ctrl_y = (var_start[1] + var_end[1]) / 2 + + def bez(t: float) -> tuple[float, float]: + x = (1 - t) ** 2 * var_start[0] + 2 * (1 - t) * t * ctrl_x + t ** 2 * var_end[0] + y = (1 - t) ** 2 * var_start[1] + 2 * (1 - t) * t * ctrl_y + t ** 2 * var_end[1] + return x, y + + # Sample the curve densely to build an arc-length lookup + n_samples = 200 + samples = [bez(i / n_samples) for i in range(n_samples + 1)] + cum_lengths = [0.0] + for a, b in zip(samples, samples[1:]): + cum_lengths.append(cum_lengths[-1] + math.hypot(b[0] - a[0], b[1] - a[1])) + total_length = cum_lengths[-1] + + def t_for_arc(target_arc: float) -> float: + for i, L in enumerate(cum_lengths): + if L >= target_arc: + # linear interpolate t around index i + if i == 0: + return 0.0 + prev = cum_lengths[i - 1] + frac = (target_arc - prev) / (L - prev) if L > prev else 0.0 + return ((i - 1) + frac) / n_samples + return 1.0 + + # 5 residues, evenly spaced along the curve (1/6, 2/6, ..., 5/6 of total) + for k, n in enumerate(range(44, 49), start=1): + target = total_length * k / 6 + t = t_for_arc(target) + coords[str(n)] = bez(t) + + return coords + + +def build_pair_lines( + sprinzl_by_pos: dict[int, dict], + pos_to_xy: dict[int, tuple[float, float]], +) -> list[dict]: + """Compute base-pair tick lines from Sprinzl pairings.""" + label_to_pos: dict[str, int] = {} + for pos, row in sprinzl_by_pos.items(): + label = row["sprinzl_label"] + label_to_pos.setdefault(label, pos) + + canonical_pairs = [ + # acceptor stem + ("1", "72"), ("2", "71"), ("3", "70"), ("4", "69"), + ("5", "68"), ("6", "67"), ("7", "66"), + # D-stem + ("10", "25"), ("11", "24"), ("12", "23"), ("13", "22"), + # AC-stem + ("27", "43"), ("28", "42"), ("29", "41"), + ("30", "40"), ("31", "39"), + # T-stem + ("49", "65"), ("50", "64"), ("51", "63"), + ("52", "62"), ("53", "61"), + ] + + lines: list[dict] = [] + for a, b in canonical_pairs: + pa, pb = label_to_pos.get(a), label_to_pos.get(b) + if pa is None or pb is None: + continue + xa, ya = pos_to_xy[pa] + xb, yb = pos_to_xy[pb] + # base-pair tick: short segment between the two paired letter centers, + # offset so it doesn't overlap the letters. + dx, dy = xb - xa, yb - ya + L = math.hypot(dx, dy) + if L < 1e-6: + continue + ux, uy = dx / L, dy / L + pad = 2.5 + x1 = xa + ux * pad + y1 = ya + uy * pad + x2 = xb - ux * pad + y2 = yb - uy * pad + # add small character-center offset (matches plot-structure.R nuc_*_offset) + x1 += 2.375 + y1 += -2.565 + x2 += 2.375 + y2 += -2.565 + lines.append({ + "x1": round(x1, 2), + "y1": round(y1, 2), + "x2": round(x2, 2), + "y2": round(y2, 2), + }) + return lines + + +# --- SVG rendering ------------------------------------------------------ + + +SVG_HEADER = """ + + {name} + +""" + +NUC_TEXT = ( + '\n' + ' {base}\n' + '\n' +) + +PAIR_PATH = ( + '\n' +) + + +def render_svg(meta: dict, trna_name: str) -> str: + parts = [SVG_HEADER.format(w=meta["width"], h=meta["height"], name=trna_name)] + for line in meta["lines"]: + parts.append(PAIR_PATH.format(**{ + "x1": line["x1"], "y1": line["y1"], + "x2": line["x2"], "y2": line["y2"], + })) + for nuc in meta["nucleotides"]: + parts.append(NUC_TEXT.format(x=nuc["x"], y=nuc["y"], base=nuc["base"])) + parts.append("\n") + return "".join(parts) + + +if __name__ == "__main__": + sys.exit(main()) diff --git a/inst/extdata/structures/Escherichia_coli/elbow/tRNA-Ala-GGC.json b/inst/extdata/structures/Escherichia_coli/elbow/tRNA-Ala-GGC.json new file mode 100644 index 0000000..ebf223b --- /dev/null +++ b/inst/extdata/structures/Escherichia_coli/elbow/tRNA-Ala-GGC.json @@ -0,0 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"x1": 134.68, + "y1": 42.5, + "x2": 134.68, + "y2": 39.94 + } + ], + "trna_name": "tRNA-Val-TAC", + "sequence": "GGGUGAUUAGCUCAGCUGGGAGAGCACCUCCCUUACAAGGAGGGGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA", + "structure": "<<<<<<<..<<<<........>>>>.<<<<<.......>>>>>.....<<<<<.......>>>>>>>>>>>>...." +} \ No newline at end of file diff --git a/inst/extdata/structures/Escherichia_coli/elbow/tRNA-Val-TAC.svg b/inst/extdata/structures/Escherichia_coli/elbow/tRNA-Val-TAC.svg new file mode 100644 index 0000000..79d841f --- /dev/null +++ b/inst/extdata/structures/Escherichia_coli/elbow/tRNA-Val-TAC.svg @@ -0,0 +1,261 @@ + + + tRNA-Val-TAC + + + + + + + + + + + + + + + + + + + + + + + + G + + + G + + + G + + + U + + + G + + + A + + + U + + + U + + + A + + + G + + + C + + + U + + + C + + + A + + + G + + + C + + + U + + + G + + + G + + + G + + + A + + + G + + + A + + + G + + + C + + + A + + + C + + + C + + + U + + + C + + + C + + + C + + + U + + + U + + + A + + + C + + + A + + + A + + + G + + + G + + + A + + + G + + + G + + + G + + + G + + + G + + + U + + + C + + + G + + + G + + + C + + + G + + + G + + + U + + + U + + + C + + + G + + + A + + + U + + + C + + + C + + + C + + + G + + + U + + + C + + + A + + + U + + + C + + + A + + + C + + + C + + + C + + + A + + + C + + + C + + + A + + diff --git a/man/plot_tRNA_structure.Rd b/man/plot_tRNA_structure.Rd index 36ed9b6..65f2be1 100644 --- a/man/plot_tRNA_structure.Rd +++ b/man/plot_tRNA_structure.Rd @@ -15,7 +15,8 @@ plot_tRNA_structure( outline_palette = NULL, text_colors = NULL, position_markers = TRUE, - linkage_palette = c("#0072B2", "#D55E00") + linkage_palette = c("#0072B2", "#D55E00"), + layout = c("cloverleaf", "elbow") ) } \arguments{ @@ -64,6 +65,13 @@ colors for negative (exclusive) and positive (co-occurring) linkage values. Default \code{c("#0072B2", "#D55E00")} (blue for exclusive, vermillion for co-occurring). Stroke width encodes the magnitude of the value.} + +\item{layout}{One of \code{"cloverleaf"} (default) or \code{"elbow"}. +\code{"elbow"} renders the L-shaped depiction with the acceptor stem +and T-arm stacked coaxially at the top, the D-arm extending +horizontally, and the anticodon arm hanging vertically. The +elbow form is currently available for E. coli standard +3-arm tRNAs.} } \value{ The path to the annotated SVG file (invisibly). @@ -78,5 +86,6 @@ linkages are drawn as Bezier curve arcs between position pairs. \examples{ \donttest{ plot_tRNA_structure("tRNA-Glu-TTC", "Escherichia coli") +plot_tRNA_structure("tRNA-Phe-GAA", "Escherichia coli", layout = "elbow") } } diff --git a/man/structure_trnas.Rd b/man/structure_trnas.Rd index 2c7764c..576722f 100644 --- a/man/structure_trnas.Rd +++ b/man/structure_trnas.Rd @@ -4,20 +4,24 @@ \alias{structure_trnas} \title{List available tRNA structures for an organism} \usage{ -structure_trnas(organism) +structure_trnas(organism, layout = c("cloverleaf", "elbow")) } \arguments{ \item{organism}{Character string specifying the organism name (e.g., \code{"Escherichia coli"}). Use \code{\link[=structure_organisms]{structure_organisms()}} to list available organisms.} + +\item{layout}{One of \code{"cloverleaf"} (default) or \code{"elbow"}. The +elbow form is currently bundled for E. coli standard tRNAs only.} } \value{ A character vector of tRNA names. } \description{ -Returns the names of tRNAs for which cloverleaf structure SVGs -are bundled with the package for the given organism. +Returns the names of tRNAs for which structure SVGs are bundled with +the package for the given organism and layout. } \examples{ structure_trnas("Escherichia coli") +structure_trnas("Escherichia coli", layout = "elbow") } diff --git a/tests/testthat/_snaps/plot-structure.md b/tests/testthat/_snaps/plot-structure.md index 11a38c1..ca9f762 100644 --- a/tests/testthat/_snaps/plot-structure.md +++ b/tests/testthat/_snaps/plot-structure.md @@ -22,22 +22,23 @@ plot_tRNA_structure("tRNA-Fake-XXX", org) Condition Error in `plot_tRNA_structure()`: - ! No structure SVG found for "tRNA-Fake-XXX". - i Use `structure_trnas()` to list available tRNAs. + ! No cloverleaf structure SVG found for "tRNA-Fake-XXX". + i Use `structure_trnas("Escherichia coli", layout = "cloverleaf")` to list available tRNAs. -# structure_to_png errors for missing file +# structure_html errors on missing file Code - structure_to_png("nonexistent.svg") + structure_html("nonexistent.svg") Condition - Error in `structure_to_png()`: + Error in `structure_html()`: ! SVG file not found: 'nonexistent.svg'. -# structure_html errors on missing file +# plot_tRNA_structure(layout = 'elbow') errors clearly when missing Code - structure_html("nonexistent.svg") + plot_tRNA_structure("tRNA-Leu-CAA", "Escherichia coli", layout = "elbow") Condition - Error in `structure_html()`: - ! SVG file not found: 'nonexistent.svg'. + Error in `plot_tRNA_structure()`: + ! No elbow structure SVG found for "tRNA-Leu-CAA". + i Use `structure_trnas("Escherichia coli", layout = "elbow")` to list available tRNAs. diff --git a/tests/testthat/test-plot-structure.R b/tests/testthat/test-plot-structure.R index 083ec9b..0389d9a 100644 --- a/tests/testthat/test-plot-structure.R +++ b/tests/testthat/test-plot-structure.R @@ -291,3 +291,53 @@ test_that("plot_tRNA_structure respects position_markers = FALSE", { end_labels <- xml2::xml_find_first(doc, ".//*[@id='clover-end-labels']") expect_false(is.na(end_labels)) }) + +# Elbow layout ---------------------------------------------------------------- + +test_that("structure_trnas(layout = 'elbow') lists bundled elbow tRNAs", { + trnas <- structure_trnas("Escherichia coli", layout = "elbow") + expect_type(trnas, "character") + expect_true(length(trnas) > 0) + # variable-arm tRNAs (Leu, Ser, SeC) are deferred to v2 + expect_false(any(grepl("^tRNA-(Leu|Ser|SeC)-", trnas))) +}) + +test_that("plot_tRNA_structure renders elbow layout SVG", { + trnas <- structure_trnas("Escherichia coli", layout = "elbow") + skip_if(length(trnas) == 0, "No bundled elbow structures") + out <- plot_tRNA_structure( + "tRNA-Phe-GAA", + "Escherichia coli", + layout = "elbow" + ) + expect_true(file.exists(out)) + doc <- xml2::read_xml(out) + texts <- xml2::xml_find_all(doc, ".//*[local-name()='text']") + expect_true(length(texts) > 70) # 76 nucleotides plus title +}) + +test_that("plot_tRNA_structure(layout = 'elbow') errors clearly when missing", { + expect_snapshot( + plot_tRNA_structure( + "tRNA-Leu-CAA", + "Escherichia coli", + layout = "elbow" + ), + error = TRUE + ) +}) + +test_that("plot_tRNA_structure(layout = 'elbow') applies modification overlay", { + trnas <- structure_trnas("Escherichia coli", layout = "elbow") + skip_if(length(trnas) == 0, "No bundled elbow structures") + mods <- dplyr::tibble(pos = c(34L, 37L), mod1 = c("m1A", "m7G")) + out <- plot_tRNA_structure( + "tRNA-Phe-GAA", + "Escherichia coli", + modifications = mods, + layout = "elbow" + ) + doc <- xml2::read_xml(out) + circles <- xml2::xml_find_all(doc, ".//*[local-name()='circle']") + expect_gte(length(circles), 2) +})