motiflogo: A new representation of DNA motif logo

In zhilongjia/motiflogo: motiflogo: A new representation of motif logo

Description

A new representation of DNA motif logo via ggplot2. Besides, the xlabel could be DNA or SNP.

Usage

motiflogo(pwm, xlabel = NULL, ylabel = "Bits", tit = "Motif",
  addpoint = FALSE, scaleSize = c(5, 20))

Arguments

pwm	position weight matrix
xlabel	text of label in x-axis
ylabel	The default is Bits
tit	The default is Motif
addpoint	add point to the position of nt. The default is FALSE
scaleSize	the scale size of nt. ref scale_size

Author(s)

Zhilong Jia

Examples

library(motiflogo)
pfm <- matrix(data=c(5, 3, 16, 1, 0, 17, 17, 0, 0, 16, 12, 8,
6, 9, 1, 1, 18,  1, 0, 0, 18,  1, 0, 2,
2,3, 1, 0, 0, 0, 0, 1, 0, 0, 1, 2,
5, 3, 0, 16, 0, 0, 1, 17,  0, 1, 5, 6),
byrow=TRUE,nrow=4,dimnames=list(c('A','C','G','T')))

pwm <- apply(pfm, 2, function(x) x/sum(x))

motiflogo(pwm)

xlabel <- c("T", "G", "A", "T", "C", "A\nC", "A", "A", "C","A", "A", "T")
motiflogo(pwm, xlabel=xlabel)
motiflogo(pwm, xlabel=xlabel, addpoint=TRUE)

zhilongjia/motiflogo documentation built on May 4, 2019, 11:22 p.m.