ABSSeq (version 1.8.0)

plotDifftoBase: Plot absolute log2 fold-change against base mean of expression

Description

Plot absolute differencs against expression levels

Usage

plotDifftoBase(object, foldname = "foldChange", adj.pcut = 0.05, cols = c("black", "red"), pch = 16, xlab = "log2 of Expression level", ylab = "log2 fold-change", ...)

Arguments

object

a ABSDataSet

foldname

indicates kind of fold-change in plotting, default is 'foldChange', see results

adj.pcut

cutoff for differential expressed genes, marked by different color, default is 0.05

cols

the colors to mark the non-DE and DE genes, defualt is black and red, respectively

pch

pch, default is 16

xlab

xlab, default is 'log2 of Expression level'

ylab

ylab, default is 'log2 fold-change'

...,

further arguments to plot

Details

Plot absolute differencs against expression levels and mark the gene with a color at a given cutoff of fold-change

Examples

data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- ABSSeq(obj)
plotDifftoBase(obj)