plotVolcano: Make an informative volcano plot using edgeR/DESeq2 output

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

Make an informative volcano plot using edgeR/DESeq2 output

Usage

plotVolcano(DEoutput, fdr = 0.05, foldChangeLine = NULL, markGenes = NULL,
  colorGenes = NULL, useGeneNames = TRUE, outFile = NULL)

Arguments

DEoutput	Tab-seperated edgeR/DESeq2 output file, using EdgeR_wrapper or DESeq_wrapper
fdr	FDR cutoff for plotting
foldChangeLine	Where to place a line for a fold change cutoff. Needs two values (for positive andnegative fold change). Default is to plot no line
markGenes	geneIDs for the genes to mark (a circle with gene name will be added)
colorGenes	geneIDs for the genes to color
useGeneNames	Use gene names instead of default geneIDs. only works if the input has been annotated by annotate_DEoutput function.
outFile	Name of output pdf file

Value

A pdf file with volcano plot

Examples

deout <- system.file("extdata", "edgeR_output_annotated.tsv", package="vivlib")
plotVolcano(deout, fdr = 0.05, foldChangeLine = NULL, markGenes = NULL,
             colorGenes = NULL, useGeneNames = TRUE, outFile = "volcano.pdf")

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.