degVolcano {DEGreport} | R Documentation

## 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,])

[Package DEGreport version 1.18.1 Index]