plot motif over another motif

Description

plot motif over another motif to emphesize the difference.

Usage

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plotMotifOverMotif(motif, backgroundMotif, bgNoise=NA, 
                font="Helvetica-Bold", textgp=gpar())

Arguments

motif

an object of pcm or pfm

backgroundMotif

an object of pcm or pfm

bgNoise

if it is not NA, test will using a background by Dirichlet(1)-distributed random frequencies with weight bg.noise. The value of bgNoise should be a number in the range of 0 to 1, eg. 0.05

font

font for logo symbol

textgp

text parameter

Value

none

Examples

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pcms <- readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
len <- sapply(pcms, function(.ele) ncol(.ele$mat))
pcms <- pcms[len==7]
plotMotifOverMotif(pcms[[1]], pcms[[2]], bgNoise=0.05)

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