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Plot a Volcano Plot for Differential Expression Results

plot_volcano.Rd

This function generates a volcano plot based on log fold changes (logFC) and adjusted p-values from differential expression analysis. It highlights genes that pass the specified thresholds for logFC and FDR (false discovery rate). Optionally, it can label genes of interest or the top up/downregulated genes.

Usage

plot_volcano(
  DT.original,
  label_col = NULL,
  lfc_threshold = 1,
  fdr_threshold = 0.01,
  labelgene = NULL
)

Arguments

DT.original

A data frame containing the differential expression results. It should have columns logFC (log fold change) and adj.P.Val (adjusted p-value).

label_col

The column name (as a string) used for labeling genes in the plot. Default is NULL. If NULL, the function will select the first column of DT.original for labeling.

lfc_threshold

A numeric value representing the threshold for log fold change (default is 1). Genes with logFC greater than or equal to this value are labeled as "UP", and genes with logFC less than or equal to the negative of this value are labeled as "DOWN".

fdr_threshold

A numeric value representing the false discovery rate (FDR) threshold (default is 0.01). Genes with an adjusted p-value greater than or equal to this threshold will be labeled as "Others".

labelgene

A character vector of gene names to be labeled in the plot (default is NULL). If provided, only these genes will be labeled in the plot.

Value

A ggplot2 object representing the volcano plot.