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

Description Usage Arguments Details Value Author(s) Examples

View source: R/volcanoPlot.R

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",
  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

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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,])

DEGreport documentation built on Nov. 17, 2017, 1:23 p.m.