Confusion Matrix Heatmap (ggplot2) — benchmark_confusion

Heatmap of Comparisons x (TP%, FP%, FN%, TN%) with white-to-blue gradient.

Usage

benchmark_confusion_gg(
  confusion_df,
  title = "Confusion Matrix by Comparison x Species",
  text_size = 3.5,
  axis_text_size = 10
)

Arguments

confusion_df: Data frame from .confusion_by_species()
title: Plot title
text_size: Size of cell text labels
axis_text_size: Size of axis text

Value

ggplot2 object

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$PG.ProteinGroups)]
ev <- data.frame(Comparison = rep(c("B-A", "D-A"), each = 2),
                 Species = c("ECOLI", "YEAST"),
                 expected_logFC = c(1, -0.58, 2, -3.3))
bench <- benchmarking_proteomics(de, ev, verbose = FALSE)
benchmark_confusion_gg(bench$confusion_by_species)