prot.plot_volcano: Plots a volcano plot for a given contrast

In NicWir/VisomX: User-Friendly and Comprehensive Analysis and Visualization of Omics Data

Plots a volcano plot for a given contrast

Description

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

NicWir/VisomX documentation built on Dec. 8, 2024, 1:27 a.m.