Significant Proteins Stacked Bars (ggplot2) — benchmark_signif_bars

Stacked bar chart of significant proteins by species, faceted by direction (UP/DOWN).

Usage

benchmark_signif_bars_gg(
  classified_df,
  ev = NULL,
  species_colors = NULL,
  title = "Significant Proteins by Species and Direction"
)

Arguments

classified_df: Classified data frame
ev: Ignored, kept for backwards compatibility with earlier calls
species_colors: Named vector of colors per species (optional)
title: Plot title

Value

ggplot2 object

Details

Counts every protein the pipeline called significant, whatever the direction. A spike-in found significant with the sign inverted is an FN, so it carries predicted = 0, but it is still a significant protein and belongs in the facet its observed logFC points to – which is precisely the facet that reveals the problem.

Examples

data(nadia_dia)
de <- process_proteomics(nadia_dia, verbose = FALSE)$DEPs_results
sp <- utils::read.delim(system.file("extdata", "nadia_dia_spikein.tsv.gz",
                                    package = "NADIA"))
de$Species <- sp$PG.OrganismId[match(de$Protein.IDs, sp$PG.ProteinGroups)]
ev <- data.frame(Comparison = rep(c("B-A", "D-A"), each = 2),
                 Species = c("ECOLI", "YEAST"),
                 expected_logFC = c(1, -0.58, 2, -3.3))
bench <- benchmarking_proteomics(de, ev, verbose = FALSE)
benchmark_signif_bars_gg(bench$classified_df, ev)