plotMotifLogo {motifStack} | R Documentation |
plot amino acid or DNA sequence logo
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, newpage=TRUE, margins=c(4.1, 4.1, 2.1, .1))
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. |
newpage |
logical If TRUE, plot it in a new page. |
margins |
A numeric vector interpreted in the same way as par(mar) in base graphics. |
none
pcm<-matrix(runif(40,0,100),nrow=4,ncol=10) pfm<-pcm2pfm(pcm) rownames(pfm)<-c("A","C","G","T") plotMotifLogo(pfm)