diffLogo: Draw DiffLogo

Description Usage Arguments Value Author(s) Examples

Description

Draws the difference of two sequence logos.

Usage

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(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

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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)
(diffLogoObj)

Example output

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

Attaching package:proxyThe following objects are masked frompackage:stats:

    as.dist, dist

The following object is masked frompackage: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.