Plot per-tRNA charging ratios. — plot_charging

Create a box-and-jitter plot of raw charging ratios grouped by condition. Expects the tibble stored in metadata(se)$charging_ratios.

Usage

plot_charging_ratios(
  data,
  group_col = "condition",
  facet_col = NULL,
  shorten = TRUE,
  point_size = 0.8,
  point_alpha = 0.4
)

Arguments

data: A tibble with at least ref, charging_ratio, and the column named by group_col.
group_col: Column name (string) for the x-axis grouping variable (e.g., "condition"). Default "condition".
facet_col: Optional column name (string) for faceting (e.g., "strain"). Default NULL.
shorten: Logical; if TRUE (default), shorten tRNA names on the y-axis via shorten_trna_names().
point_size: Numeric size for ggplot2::geom_jitter(). Default 0.8.
point_alpha: Numeric alpha for jittered points. Default 0.4.

Value

A ggplot object.

Examples

df <- tibble::tibble(
  ref = rep(paste0("tRNA-Ala-AGC-", 1:3, "-1"), each = 6),
  condition = rep(c("ctl", "inf"), each = 3, times = 3),
  charging_ratio = runif(18, 0.3, 0.9)
)
plot_charging_ratios(df)