metabolomics (version 0.1.4)

VolcanoPlot: Volcano plot

Description

Produces a volcano plot given fold changes and p-values.

Usage

VolcanoPlot(folds, pvals, cexcutoff = 0.7, cexlab = 0.5, plimit = 0.05,  fclimit = 2, xlab = 'log2 Fold Change', ylab = '-log10 t-Test P-value', main = "Volcano Plot", ...)

Arguments

folds

A vector of fold changes with metabolite names.

pvals

A vector of corresponding p-values with metabolite names.

cexcutoff

Font size of the cut-off labels.

cexlab

Font size of the variable labels.

plimit

A numeric indicating the p value cutoff. The default is set to 0.05.

fclimit

A numeric indicating the lower fold cutoff. The default is set to 2.

xlab

x-axis label.

ylab

y-axis label

main

Plot title.

...

Other graphical parameters. See par.

See Also

TwoGroup, TwoGroupPlots.

Examples

    data(treated)
    treated.log <- LogTransform(treated, base = 2)$output
    results <- TwoGroup(treated.log)$output
    pval <- results[, 2]
    fc <- results[, 4]
    VolcanoPlot(fc, pval, cexlab = 0.8)