seqLogo: Draw sequence logo

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

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)

Example output

Loading required package: cba
Loading required package: grid
Loading required package: proxy

Attaching package: ‘proxy’

The following objects are masked from ‘package:stats’:

    as.dist, dist

The following object is masked from ‘package:base’:

    as.matrix

[1] "pwm must be of class matrix or data.frame. Trying to convert"

DiffLogo documentation built on Nov. 8, 2020, 6:09 p.m.