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Plot Volcano Plot for Differential Expression Analysis

Source: R/differential_expression.R
plotVolcano.Rd

plotVolcano generates a volcano plot to visualize differential expression results.

Usage

plotVolcano(tableDE, pFilter = 0.05, fcFilter = 0.5)

Arguments

tableDE

A data frame containing differential expression results with columns 'ID', 'log2FC', 'pvalue', and 'Gene'.

pFilter

A numeric value specifying the p-value threshold for significance. Default is 0.05.

fcFilter

A numeric value specifying the log2 fold-change threshold for significance. Default is 0.5.

Value

A ggplot2 object representing the volcano plot.

Details

This function creates a volcano plot where differentially expressed genes are categorized as 'Up', 'Down', or 'Not Sig' based on the provided p-value and log2 fold-change thresholds. Points on the plot are color-coded to indicate their expression status.

Examples

library(SummarizedExperiment)
# Load multiAssayExperiment object
data("dda_example")
# Get SummarizedExperiment object
se <- dda_example[["Proteome"]]
colData(se) <- colData(dda_example)
# Preprocess the proteome assay
result <- preprocessProteome(se, normalize = TRUE)
# Call the function to perform differential expression analyis
de <- performDifferentialExp(se = result, assay = "Intensity",
method = "limma", reference = "1stCrtl", target = "EGF",
condition = "treatment")
# Plot the volcano plot from the result
plotVolcano(de$resDE)