kuva volcano
Volcano plot for differential expression results.
Input: three columns — gene name, log₂ fold change, raw p-value.
| Flag | Default | Description |
|---|---|---|
--name-col <COL> | 0 | Gene/feature name column |
--x-col <COL> | 1 | log₂FC column |
--y-col <COL> | 2 | p-value column (raw, not −log₁₀) |
--pvalue-col-is-log | off | p-value column already contains −log₁₀(p); un-transform before plotting |
--fc-cutoff <F> | 1.0 | |log₂FC| threshold |
--p-cutoff <F> | 0.05 | p-value significance threshold |
--top-n <N> | 0 | Label the N most-significant points |
--color-up <CSS> | firebrick | Up-regulated point color |
--color-down <CSS> | steelblue | Down-regulated point color |
--color-ns <CSS> | #aaaaaa | Not-significant point color |
--point-size <PX> | 3.0 | Point radius |
--legend | off | Show Up / Down / NS legend |
kuva volcano gene_stats.tsv \
--name-col gene --x-col log2fc --y-col pvalue \
--top-n 20 --legend
kuva volcano gene_stats.tsv \
--name-col gene --x-col log2fc --y-col pvalue \
--fc-cutoff 2.0 --p-cutoff 0.01 --top-n 10
# when p-value column already holds -log10(p)
kuva volcano results.tsv --name-col gene --x-col log2fc --y-col neg_log10_p \
--pvalue-col-is-log
See also: Shared flags — output, appearance, axes, log scale.