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.
Arguments
- de.results
Data frame as returned by
run.limma.de(), containing at minimum the columnslogFCandadj.P.Val.- fc.threshold
Numeric. Absolute log2 fold-change cutoff for labeling genes as differentially expressed. Default is
1(i.e., 2-fold).- fdr.threshold
Numeric. Adjusted p-value cutoff. Default is
0.05.
Value
A ggplot object showing each probe as a point with logFC on
the x-axis and -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.
Details
The volcano plot is the standard summary visualization for a TopTable from
run.limma.de() and serves as the genome-wide complement to
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 analyze.gene() or inclusion in a gene
signature for run.gsea().