Performance Heatmap (ggplot2) — benchmark_heatmap

Heatmap of Comparisons x Metrics (AUC, Sensitivity, Specificity, Precision, F1, Accuracy). Gradient red -> yellow -> green.

Usage

benchmark_heatmap_gg(
  metrics_table,
  metrics_to_show = c("AUC", "Sensitivity", "Specificity", "Precision", "F1", "Accuracy"),
  title = "Benchmark Performance Heatmap",
  text_size = 4,
  axis_text_size = 11
)

Arguments

metrics_table: Data frame from compute_benchmark_metrics()
metrics_to_show: Character vector of metrics to display
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))
metrics <- compute_benchmark_metrics(de, ev)
benchmark_heatmap_gg(metrics, metrics_to_show = c("AUC", "F1", "MCC"))