Prepare data for plot_mod_heatmap().

Join Sprinzl coordinates to a bcerror delta tibble, optionally annotate known modifications, order positions by canonical Sprinzl index, and shorten tRNA names for display.

Usage

prep_mod_heatmap(
  data,
  value_col = "delta",
  ref_col = "ref",
  sprinzl_coords,
  mods = NULL,
  strip_prefix = "^host-",
  shorten_labels = TRUE
)

Arguments

data

A tibble with at least ref, pos, and a value column (e.g., delta from compute_bcerror_delta()).

value_col

Column name (string) for the fill value. Default "delta".

ref_col

Column name (string) for the tRNA reference. Default "ref".

sprinzl_coords

A tibble of Sprinzl coordinates from read_sprinzl_coords(), with at least trna_id, pos, sprinzl_label, and global_index columns.

mods

Optional tibble of modification annotations (e.g., from modomics_mods()) with at least ref and pos columns. When provided, a logical has_mod column is added.

strip_prefix

Regex pattern to strip from ref before matching Sprinzl coordinates. Default "^host-".

shorten_labels

Logical; if TRUE (default), create a trna_label column with shortened names (e.g., "tRNA-Glu-TTC-1-1" becomes "Glu-TTC").

Value

A tibble ready for plot_mod_heatmap(), with sprinzl_label as an ordered factor and optionally has_mod and trna_label columns.

Examples

if (FALSE) { # \dontrun{
bcerror_delta <- compute_bcerror_delta(bcerror_summary, delta = wt - tb)
sprinzl <- read_sprinzl_coords(
  clover_example("sprinzl/ecoliK12_global_coords.tsv.gz")
)
mods <- modomics_mods(trna_fasta, organism = "Escherichia coli")
heatmap_data <- prep_mod_heatmap(
  bcerror_delta,
  sprinzl_coords = sprinzl,
  mods = mods
)
} # }