Interactive Volcano Plot with Highcharter

Usage

volcano_highchart_list(
  de_res,
  ain = NULL,
  comparisons = NULL,
  lfc_thr = 0,
  alpha = 0.05,
  p_col = "adj.P.Val",
  point_size = 4,
  colors = NULL,
  palette = NULL,
  show_top_genes = 0,
  highlight_genes = NULL,
  title = NULL
)

Arguments

de_res: Data frame with differential expression results
ain: Vector of assays to filter on (optional)
comparisons: Vector of comparisons to include (optional)
lfc_thr: log2 fold-change threshold (default: 0)
alpha: Significance threshold (default: 0.05)
p_col: Column of p-values to use
point_size: Point size (default: 4)
colors: List of colours for "up", "down", "ns" (ignored when palette is used)
palette: Name of a paletteer palette (e.g. "ggsci::default_jco"). Uses 3 colours: up, down, ns
show_top_genes: Number of top genes to label by significance (default: 0)
highlight_genes: Vector of gene names to highlight manually (default: NULL)
title: Custom chart title (default: NULL, uses "Comparison (Assay)"). Use {comparison} as a placeholder (e.g. "Volcano Plot: {comparison}" -> "Volcano Plot: B-A")

Value

List of highchart objects

Examples

data(nadia_dia)
res <- process_proteomics(nadia_dia, verbose = FALSE)

# One volcano per comparison, labelling the 10 most significant proteins
hc_list <- volcano_highchart_list(
  res$DEPs_results,
  comparisons     = c("B-A", "D-A"),
  lfc_thr         = 1,
  alpha           = 0.05,
  show_top_genes  = 10
)
names(hc_list)
#> [1] "B-A" "D-A"