plot motif over another motif

Description

plot motif over another motif to emphesize the difference.

Usage

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

Arguments

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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(motifStack)
Loading required package: grImport
Loading required package: grid
Loading required package: XML
Loading required package: MotIV
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit


Attaching package: 'MotIV'

The following object is masked from 'package:stats':

    filter

Loading required package: ade4

Attaching package: 'ade4'

The following object is masked from 'package:BiocGenerics':

    score

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/motifStack/plotMotifOverMotif.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifOverMotif
> ### Title: plot motif over another motif
> ### Aliases: plotMotifOverMotif
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>