The Volcano plot function for all APAF scripts

The Volcano plot function for all APAF scripts

Usage

plotVolcano(
  experiment = c("SWATH", "TMT"),
  FC,
  pval,
  names,
  PeporProt = c("Peptide", "Protein"),
  comp.idx,
  FCcutoff = 1.5,
  pvalcutoff = 0.05,
  saveInteractive = TRUE
)

Arguments

experiment

SWATH or TMT

PeporProt

Specify 'Protein' or 'Peptide' depending on the plot. No other options are accepted

FCcutoff

Fold Change cut off. Should be passed in from the script environment, but defaults to 1.5

interactive

TRUE or FALSE to plot an interactive volcano plot into a HTML file