Plots a volcano plot for a given contrast

Usage

prot.plot_volcano(
  dep,
  contrast,
  label_size = 3,
  alpha = 0.05,
  lfc = 2,
  add_names = TRUE,
  adjusted = FALSE,
  plot = TRUE,
  export = TRUE
)

Arguments

dep: A SummarizedExperiment object
contrast: The contrast of interest in the format "conditionA_vs_conditionB"
label_size: The size of labels for the protein names
alpha: The alpha value used to determine significance.
lfc: The log2 fold change threshold.
add_names: Logical, whether to add protein names to the plot
adjusted: Logical, whether to plot adjusted p-values. The alpha threshold is applied to adjusted p values even if adjusted = FALSE.
plot: Logical, whether to return the volcano plot
export: Logical, whether to export the volcano plot as PND and PDF file

Value

(invisibly) A data frame with columns for protein, log2 fold change, and -log10 p-value