Last data update: 2014.03.03

 R: Volcano plot
VolcanoPlotR Documentation

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.

Author(s)

Alysha M De Livera, Jairus B Bowne

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)

Results


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO