% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/visualization.R
\name{volcano.plot}
\alias{volcano.plot}
\title{Plot Volcano Plot from Differential Expression Results}
\usage{
volcano.plot(de.results, fc.threshold = 1, fdr.threshold = 0.05)
}
\arguments{
\item{de.results}{Data frame as returned by \code{run.limma.de()}, containing
at minimum the columns \code{logFC} and \code{adj.P.Val}.}

\item{fc.threshold}{Numeric. Absolute log2 fold-change cutoff for labeling
genes as differentially expressed. Default is \code{1} (i.e., 2-fold).}

\item{fdr.threshold}{Numeric. Adjusted p-value cutoff. Default is \code{0.05}.}
}
\value{
A ggplot object showing each probe as a point with \code{logFC} on
the x-axis and \code{-log10(adj.P.Val)} on the y-axis. Points are colored
as upregulated, downregulated, or not significant. Dashed threshold lines
are drawn at the specified cutoffs.
}
\description{
Generates a volcano plot visualizing the relationship between statistical
significance and fold-change magnitude for all probes in a differential
expression analysis. Points are colored by whether they exceed user-defined
significance and fold-change thresholds.
}
\details{
The volcano plot is the standard summary visualization for a TopTable from
\code{run.limma.de()} and serves as the genome-wide complement to
\code{gene.analysis.plot()}, which visualizes a single gene. Probes that
appear in the upper corners (high fold-change, low FDR) are the strongest
candidates for follow-up with \code{analyze.gene()} or inclusion in a gene
signature for \code{run.gsea()}.
}
