seqLogo {DiffLogo} | R Documentation

## Draw sequence logo

### Description

Draws the classic sequence logo.

### Usage

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

### 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
`main` | the main title for the plot

### Value

none (draws sequence logo)

### Author(s)

Martin Nettling

### Examples

    motif_folder= "extdata/pwm"
    motif_name = "HepG2"
    fileName = paste(motif_folder,"/",motif_name,".pwm",sep="")
    file = system.file(fileName, package = "DiffLogo")
    motif = getPwmFromPwmFile(file)
    seqLogo(pwm = motif)

[Package DiffLogo version 2.4.0 Index]