Plot abundance changes versus charging ratio changes. — plot_abundance

Creates a scatter plot comparing tRNA abundance changes (from DESeq2) with charging ratio changes on a single plot. Significant points are colored by quadrant and labeled with ggrepel::geom_text_repel().

Usage

plot_abundance_charging(
  deseq_res,
  charging_diffs,
  lab_col = "ref",
  padj_cutoff = 0.05,
  max_overlaps = 20,
  point_size = 2,
  label_size = 3,
  shorten = TRUE,
  source_col = NULL,
  error_bars = TRUE
)

Arguments

deseq_res: A tibble from tidy_deseq_results() with at least ref, log2FoldChange, and padj columns. When error_bars is TRUE, an lfcSE column is also expected.
charging_diffs: A tibble from compute_charging_diffs() with at least ref and diff columns.
lab_col: Column name (string) used for point labels. Default "ref".
padj_cutoff: Numeric; significance threshold for padj. Default 0.05.
max_overlaps: Maximum number of overlapping labels passed to ggrepel::geom_text_repel(). Default 20.
point_size: Numeric size for ggplot2::geom_point(). Default 2.
label_size: Numeric size for ggrepel::geom_text_repel(). Default 3.
shorten: Logical; if TRUE (default), shorten tRNA names in point labels via shorten_trna_names().
source_col: Optional column name (string) for faceting, e.g., "source" to separate host and phage tRNAs. When provided, the column must exist in deseq_res. Default NULL.
error_bars: Logical; if TRUE (default), draw horizontal error bars (lfcSE) on significant points. Requires an lfcSE column in deseq_res.

Value

A ggplot object.

Examples

deseq_res <- tibble::tibble(
  ref = paste0("tRNA-", 1:6),
  log2FoldChange = c(1, -1, 0.5, -0.5, 2, -2),
  padj = c(0.01, 0.02, 0.5, 0.6, 0.001, 0.003)
)
charging_diffs <- tibble::tibble(
  ref = paste0("tRNA-", 1:6),
  diff = c(0.1, -0.1, 0.05, -0.05, -0.2, 0.15),
  se_diff = rep(0.03, 6)
)
plot_abundance_charging(deseq_res, charging_diffs)