diffLogo: Draw DiffLogo

In DiffLogo: DiffLogo: A comparative visualisation of biooligomer motifs

Description

Draws the difference of two sequence logos.

Usage

diffLogo(diffLogoObj, ymin = 0, ymax = 0, sparse = FALSE,
  diffLogoConfiguration = list())

Arguments

diffLogoObj	a DiffLogoObject created by the function createDiffLogoObject
ymin	minimum value on the y-axis
ymax	maximum value on the y-axis
sparse	if TRUE margins are reduced and tickmarks are removed from the logo
diffLogoConfiguration	list of configuration parameters (see function diffLogoTableConfiguration(...))

Value

none (draws difference logo)

Author(s)

Martin Nettling

Examples

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

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

diffLogoObj = createDiffLogoObject(pwm1 = pwm1, pwm2 = pwm2)
diffLogo(diffLogoObj)

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

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