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Prepare data for plot_mod_heatmap().

Source: R/plots.R
prep_mod_heatmap.Rd

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

bcerror_rds <- readRDS(clover_example("ecoli/bcerror_summary.rds"))
bcerror_delta <- compute_bcerror_delta(
  bcerror_rds$bcerror_summary, delta = wt - tb
)
sprinzl <- read_sprinzl_coords(
  clover_example("sprinzl/ecoliK12_global_coords.tsv.gz")
)
prep_mod_heatmap(bcerror_delta, sprinzl_coords = sprinzl)
#> # A tibble: 776 × 9
#>    ref             pos     tb     wt    delta trna_id sprinzl_label global_index
#>    <chr>         <dbl>  <dbl>  <dbl>    <dbl> <chr>   <fct>                <dbl>
#>  1 tRNA-Asn-GTT…     1 0.0334 0.0405  7.11e-3 tRNA-A… 1                        1
#>  2 tRNA-Asn-GTT…     2 0.0660 0.0896  2.36e-2 tRNA-A… 2                        3
#>  3 tRNA-Asn-GTT…     3 0.0587 0.0809  2.21e-2 tRNA-A… 3                        4
#>  4 tRNA-Asn-GTT…     4 0.195  0.201   5.84e-3 tRNA-A… 4                        8
#>  5 tRNA-Asn-GTT…     5 0.258  0.288   2.92e-2 tRNA-A… 5                        9
#>  6 tRNA-Asn-GTT…     6 0.117  0.134   1.70e-2 tRNA-A… 6                       11
#>  7 tRNA-Asn-GTT…     7 0.125  0.133   7.20e-3 tRNA-A… 7                       12
#>  8 tRNA-Asn-GTT…     8 0.0644 0.0706  6.17e-3 tRNA-A… 8                       13
#>  9 tRNA-Asn-GTT…     9 0.0623 0.0619 -3.87e-4 tRNA-A… 9                       14
#> 10 tRNA-Asn-GTT…    10 0.0295 0.0266 -2.95e-3 tRNA-A… 10                      15
#> # ℹ 766 more rows
#> # ℹ 1 more variable: trna_label <chr>