| plotMotifLogo {motifStack} | R Documentation |
plot amino acid or DNA sequence logo
plotMotifLogo(
pfm,
motifName,
p = rep(0.25, 4),
font = "Helvetica-Bold",
fontface = "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, 0.1),
draw = TRUE
)
pfm |
a position frequency matrices |
motifName |
motif name |
p |
background possibility |
font |
font of logo |
fontface |
fontface 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. |
draw |
Vector (logical(1)). TRUE to plot. FALSE, return a gList |
none
pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
plotMotifLogo(pfm)