motifStack (version 1.16.2)

plotMotifLogoA: plot sequence logo without plot.new

Description

plot amino acid or DNA sequence logo in a given canvas

Usage

plotMotifLogoA(pfm, font="Helvetica-Bold", ic.scale=TRUE, fontsize=12)

Arguments

pfm

an object of pfm

font

font of logo

ic.scale

logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.

fontsize

font size of the template for grImport, default 12. Higher value make better quality figure, but also increase the file size.

Value

• none

Examples

pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
motif <- new("pfm", mat=pfm, name="bin_SOLEXA")
plotMotifLogoA(motif)