diffLogoFromPwm: Draw DiffLogo from PWM

Description Usage Arguments Value Author(s) Examples

View source: R/diffSeqLogo.R

Description

Draws the difference of two sequence logos.

Usage

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diffLogoFromPwm(pwm1, pwm2, ymin = 0, ymax = 0,
  stackHeight = shannonDivergence,
  baseDistribution = normalizedDifferenceOfProbabilities, sparse = FALSE,
  alphabet = DNA, align_pwms = FALSE,
  unaligned_penalty = divergencePenaltyForUnaligned,
  try_reverse_complement = TRUE, base_distribution = NULL,
  length_normalization = FALSE)

Arguments

pwm1

representation of the first position weight matrix (PWM) of type pwm, data.frame, or matrix

pwm2

representation of the second position weight matrix (PWM) of type pwm, data.frame, or matrix

ymin

minimum value on the y-axis

ymax

maximum value on the y-axis

stackHeight

function for the height of a stack at position i

baseDistribution

function for the heights of the individual bases

sparse

if TRUE margins are reduced and tickmarks are removed from the logo

alphabet

of type Alphabet

align_pwms

if true, DiffLogo will align pwms before plotting

unaligned_penalty

is a function for localPwmAlignment.

try_reverse_complement

if True, alignment will try reverse complement pwms

base_distribution

is a vector of length nrow(pwm) that is added to unaligned columns of pwms for comparing. If NULL, uniform distribution is used

length_normalization

If true, will minimize the average divergence between PWMs. Otherwise will minimize the sum of divergences between positions. In both cases unalignes positions are compared to base_distribution and are counted when computing the alignment length.

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]]]]

diffLogoFromPwm(pwm1 = pwm1, pwm2 = pwm2)

DiffLogo documentation built on Nov. 1, 2018, 2:24 a.m.