degVolcano: Create volcano plot from log2FC and adjusted pvalues data...

In lpantano/DEGreport: Report of DEG analysis

Create volcano plot from log2FC and adjusted pvalues data frame

Description

Create volcano plot from log2FC and adjusted pvalues data frame

Usage

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",
  plot_text = NULL
)

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
plot_text	data.frame with three columns: logFC, Pvalue, Gene name

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.

Author(s)

Lorena Pantano, John Hutchinson

Examples

library(DESeq2)
dds <- makeExampleDESeqDataSet(betaSD = 1)
dds <- DESeq(dds)
stats <- results(dds)[,c("log2FoldChange", "padj")]
stats[["name"]] <- row.names(stats)
degVolcano(stats, plot_text = stats[1:10,])

lpantano/DEGreport documentation built on Feb. 28, 2024, 12:01 a.m.