Volcano plot colored by Species with plotLines at expected logFC values, dispersion stats in subtitle.
Usage
benchmark_volcano_hc(
de_res_comp,
ev_comp,
disp_comp = NULL,
alpha = 0.05,
lfc_thr = 0,
p_col = "adj.P.Val",
species_colors = NULL,
point_size = 3,
title = NULL,
height = NULL
)Arguments
- de_res_comp
DE results for one comparison
- ev_comp
Expected values for one comparison
- disp_comp
Dispersion metrics for one comparison (optional)
- alpha
Significance threshold
- lfc_thr
Log fold-change threshold
- p_col
P-value column
- species_colors
Named vector of colors per species
- point_size
Marker radius (default: 3)
- title
Custom title (optional)
- height
Chart height in pixels (optional)
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$PG.ProteinGroups)]
ev <- data.frame(Comparison = rep(c("B-A", "D-A"), each = 2),
Species = c("ECOLI", "YEAST"),
expected_logFC = c(1, -0.58, 2, -3.3))
disp <- compute_dispersion_metrics(de, ev)
benchmark_volcano_hc(de[de$Comparison == "B-A", ],
ev[ev$Comparison == "B-A", ],
disp_comp = disp[disp$Comparison == "B-A", ])