Static volcano plot (log2 ratio vs -log10 p)

Usage

volcano_static(
  df,
  pair = NULL,
  rank = NULL,
  color_by = NULL,
  color_title = NULL,
  fc_cut = 1,
  p_cut = 0.05,
  p_mode = c("raw", "bh"),
  significant_colors = c(`not significant` = "#386cb0", `significant prior correction` =
    "#1b9e77", `significant post fdr correction` = "#e31a1c")
)

Arguments

df: A data frame with prevalence results.
pair: optional group pair (character length-2).
rank: optional single rank (character) to keep.
color_by: optional named vector identifying peptide-library values to highlight, e.g. c("is_flagellum" = TRUE).
color_title: optional legend title when color_by is used.
fc_cut: Numeric; absolute log2 fold-change cutoff.
p_cut: Numeric; p-value cutoff.
p_mode: One of c("raw","bh"); "bh" applies BH correction per-plot from p_raw.
significant_colors: Named vector of colors for significance categories.

Value

A ggplot object.

Examples

set.seed(2)
prev <- data.frame(
  rank       = "peptide_id",
  feature    = paste0("pep", 1:40),
  group1     = "A",
  group2     = "B",
  prop1      = runif(40),
  prop2      = runif(40),
  percent1   = runif(40, 0, 100),
  percent2   = runif(40, 0, 100),
  ratio      = runif(40, 0.1, 10),
  p_raw      = c(runif(10, 0, 0.01), runif(30, 0.1, 1)),
  n_peptides = 1L
)

# basic volcano
volcano_static(prev)


# BH correction, custom cutoffs
volcano_static(prev, fc_cut = 1.5, p_cut = 0.01, p_mode = "bh")


# filter to one pair
volcano_static(prev, pair = c("A", "B"), rank = "peptide_id")