plotMotifOverMotif: plot motif over another motif

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

plot motif over another motif

Description

plot motif over another motif to emphesize the difference.

Usage

plotMotifOverMotif(
  motif,
  backgroundMotif,
  bgNoise = NA,
  font = "sans",
  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

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)

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.