Create volcano plot from log2FC and adjusted pvalues data frame

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Description

Create volcano plot from log2FC and adjusted pvalues data frame

Usage

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degVolcano(stats, side = "both",
  title = "Volcano Plot with Marginal Distributions", pval.cutoff = 0.05,
  lfc.cutoff = 1, shade.colour = "orange", shade.alpha = 0.25,
  point.colour = "gray", point.alpha = 0.75,
  point.outline.colour = "darkgray", line.colour = "gray")

Arguments

stats

data.frame with two columns: logFC and Adjusted.Pvalue

side

plot UP, DOWN or BOTH de-regulated points

title

title for the figure

pval.cutoff

cutoff for the adjusted pvalue. Default 0.05

lfc.cutoff

cutoff for the log2FC. Default 1

shade.colour

background color. Default orange.

shade.alpha

transparency value. Default 0.25

point.colour

colours for points. Default gray

point.alpha

transparency for points. Default 0.75

point.outline.colour

Default darkgray

line.colour

Defaul gray

Details

This function was mainly developed by @jnhutchinson.

Value

The function will plot volcano plot together with density of the fold change and p-values on the top and the right side of the volcano plot.

Examples

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data(DEGreportSet)
stats = DEGreportSet$deg[,c("logFC", "PValue")]
degVolcano(stats)

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