DiffLogo (version 1.2.1)

seqLogo: Draw sequence logo

Description

Draws the classic sequence logo.

Usage

seqLogo(pwm, sparse = FALSE, drawLines = 0.5, stackHeight = informationContent, baseDistribution = probabilities, alphabet = DNA)

Arguments

pwm

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

sparse

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

drawLines

distance between background lines

stackHeight

function for the height of a stack at position i

baseDistribution

function for the heights of the individual bases

alphabet

of type Alphabet

Examples

motif_folder= "extdata/pwm"
motif_name = "HepG2"
fileName = paste(motif_folder,"/",motif_name,".txt",sep="")
file = system.file(fileName, package = "DiffLogo")
motif = as.matrix(read.delim(file,header=FALSE))
seqLogo(pwm = motif)