List of Benchmark Volcano Plots (Highcharter) — benchmark_volcano_hc

Generates one volcano plot per comparison.

Usage

benchmark_volcano_hc_list(
  de_res,
  ev,
  disp = NULL,
  alpha = 0.05,
  lfc_thr = 0,
  p_col = "adj.P.Val",
  comparisons = NULL,
  assay = NULL,
  species_colors = NULL,
  point_size = 3,
  height = NULL,
  species_df = NULL
)

Arguments

de_res: Data frame with DE results
ev: Data frame with expected values
disp: Dispersion metrics data frame (optional)
alpha: Significance threshold (default: 0.05)
lfc_thr: Log fold-change threshold (default: 0)
p_col: P-value column (default: "adj.P.Val")
comparisons: Comparisons to include (NULL = all)
assay: Assay to filter (NULL = all)
species_colors: Named vector of colors per species (optional)
point_size: Marker radius (default: 3)
height: Chart height in pixels (optional)
species_df: Data frame with Protein.IDs and Species columns (optional). If NULL, de_res must already contain a Species column.

Value

Named list of highchart objects

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))
volcanoes <- benchmark_volcano_hc_list(de, ev)
names(volcanoes)
#> [1] "B-A" "D-A"
volcanoes[["B-A"]]