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Last data update: 2014.03.03

R: plot sequence logo

plotMotifLogo

R Documentation

plot sequence logo

Description

plot amino acid or DNA sequence logo

Usage

plotMotifLogo(pfm, motifName, p=rep(0.25, 4), font="Helvetica-Bold", 
colset=c("#00811B","#2000C7","#FFB32C","#D00001"), 
xaxis=TRUE,yaxis=TRUE,xlab="position",ylab="bits",
xlcex=1.2, ylcex=1.2, ncex=1.2, ic.scale=TRUE, fontsize=12)

Arguments

`pfm`	a position frequency matrices
`motifName`	motif name
`p`	background possibility
`font`	font of logo
`colset`	color setting for each logo letter
`xaxis`	draw x-axis or not
`yaxis`	draw y-axis or not
`xlab`	x-label, do nothing if set xlab as NA
`ylab`	y-label, do nothing if set ylab as NA
`xlcex`	cex value for x-label
`ylcex`	cex value for y-label
`ncex`	cex value for motif name
`ic.scale`	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.
`fontsize`	font size of the template for grImport, default 12. Higher value make better quality figure, but also increase the file size.

Value

none

Examples

pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
pfm<-pcm2pfm(pcm)
rownames(pfm)<-c("A","C","G","T")
plotMotifLogo(pfm)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/plotMotifLogo.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotMotifLogo
> ### Title: plot sequence logo
> ### Aliases: plotMotifLogo
> 
> ### ** Examples
> 
> pcm<-matrix(runif(40,0,100),nrow=4,ncol=10)
> pfm<-pcm2pfm(pcm)
> rownames(pfm)<-c("A","C","G","T")
> plotMotifLogo(pfm)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>