Volcano plot for visualizing differential metabolite analysis results

This function generates a volcano plot using data from mmo$pairwise (PairwiseComp(mmo, 'group1', 'group2') should be precended), highlighting upregulated and downregulated features based on log2 fold change and adjusted p-value

Usage

VolcanoPlot(
  mmo,
  comp,
  topk = 10,
  log2FC_thr = 1,
  pthr = 0.05,
  outdir = "volcano.png",
  height = 5,
  width = 5,
  save_output = TRUE,
  use_padj = TRUE
)

Arguments

mmo: The mmo object with pairwise comparison matrix
comp: The comparison to visualize, e.g., 'group1_vs_group2
topk: The number of top features to label in the plot (default: 10)
log2FC_thr: The threshold of log2 fold change to be considered significant (default: 1)
pthr: The threshold of adjusted p-value to be considered significant (default: 0.05)
outdir: The output file path for the volcano plot (default: 'volcano.png')
height: The height of the output plot in inches (default: 5)
width: The width of the output plot in inches (default: 5)
save_output: A logical value indicating whether to save the output plot (default: TRUE)
use_padj: A logical value indicating whether to use adjusted p-value (default: TRUE)

Value

A list containing the volcano plot and the data used to generate it

Examples

if (FALSE) {
VolcanoPlot(
 mmo, comp = 'Control_vs_Treatment1',
 topk = 10, log2FC_thr = 1, pthr = 0.05,
 outdir = 'volcano_con_tre1.png', height = 5, width = 5
)
}