motifStack (version 1.16.2)

plotMotifLogo: plot sequence logo

Description

plot amino acid or DNA sequence logo

Usage

plotMotifLogo(pfm, motifName, p=rep(0.25, 4), font="Helvetica-Bold", 
colset=c("#00811B","#2000C7","#FFB32C","#D00001"), 
xaxis=TRUE,yaxis=TRUE,xlab="position",ylab="bits",
xlcex=1.2, ylcex=1.2, ncex=1.2, ic.scale=TRUE, fontsize=12)

Arguments

pfm

a position frequency matrices

motifName

motif name

p

background possibility

font

font of logo

colset

color setting for each logo letter

xaxis

draw x-axis or not

yaxis

draw y-axis or not

xlab

x-label, do nothing if set xlab as NA

ylab

y-label, do nothing if set ylab as NA

xlcex

cex value for x-label

ylcex

cex value for y-label

ncex

cex value for motif name

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")
plotMotifLogo(pfm)