seqLogo: Draw sequence logo
In mgledi/DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description Usage Arguments Value Author(s) Examples

Draws the classic sequence logo.

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

`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

none (draws sequence logo)

Martin Nettling

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)