Version Compatibility

Reference examples tested with: DESeq2 1.42+, EnhancedVolcano 1.20+, ggplot2 3.5+, ggrepel 0.9.5+, matplotlib 3.8+, numpy 1.26+, adjustText 1.1+, apeglm 1.28+, ashr 2.2+.

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Volcano and MA Plots

"Plot differential-expression results" -> Place per-feature shrunken effect estimate on the x-axis and a significance measure (-log10 padj or -log10 p) on the y-axis. The decision space spans which effect estimate (raw vs shrunken), which significance measure (raw p vs adjusted vs s-value), how to encode categories (color by direction, not by gradient), how to label (top-N is rarely informative), and how to handle the tail (extreme p compresses the plot).

• R: EnhancedVolcano::EnhancedVolcano(), ggplot2 + ggrepel, DESeq2::plotMA()
• Python: matplotlib.scatter with adjustText, sanbomics.tools.volcano, custom seaborn

The Single Most Important Modern Insight -- Plot Shrunken LFC