DiffLogo (version 1.2.1)

diffLogoFromPwm: Draw DiffLogo from PWM

Description

Draws the difference of two sequence logos.

Usage

diffLogoFromPwm(pwm1, pwm2, ymin = 0, ymax = 0, stackHeight = shannonDivergence, baseDistribution = normalizedDifferenceOfProbabilities, sparse = FALSE, alphabet = DNA)

Arguments

pwm1

representation of the first position weight matrix (PWM) of type pwm, data.frame, or matrix

pwm2

representation of the second position weight matrix (PWM) of type pwm, data.frame, or matrix

ymin

minimum value on the y-axis

ymax

maximum value on the y-axis

stackHeight

function for the height of a stack at position i

baseDistribution

function for the heights of the individual bases

sparse

if TRUE margins are reduced and tickmarks are removed from the logo

alphabet

of type Alphabet

Examples

motif_folder= "extdata/pwm"
motif_names = c("HepG2","MCF7","HUVEC","ProgFib")
motifs = list()
for (name in motif_names) {
  fileName = paste(motif_folder,"/",name,".txt",sep="")
  file = system.file(fileName, package = "DiffLogo")
  motifs[[name]] = as.matrix(read.delim(file,header=FALSE))
}

pwm1 = motifs[[motif_names[[1]]]]
pwm2 = motifs[[motif_names[[2]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2)