plot a DNA sequence logo stack

Description

Plot a DNA sequence logo stack

Usage

motifStack(pfms, layout=c("stack", "treeview", "phylog", "radialPhylog"), ...)

Arguments

Value

return a list contains pfms and phylog

Examples

  if(interactive()){
    library("MotifDb")
    matrix.fly <- query(MotifDb, "Dmelanogaster")
    motifs <- as.list(matrix.fly)
    motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
    names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
                gsub("_FBgn[0-9]+$", "", 
                  gsub("[^a-zA-Z0-9]","_", 
                     gsub("(_[0-9]+)+$", "", names(motifs)))))
    motifs <- motifs[unique(names(motifs))]
    pfms <- sample(motifs, 50)
    pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]], name=.ele)},pfms)
    motifStack(pfms, "radialPhylog")
  }

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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
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/motifStack.Rd_%03d_medium.png", width=480, height=480)
> ### Name: motifStack
> ### Title: plot a DNA sequence logo stack
> ### Aliases: motifStack
> 
> ### ** Examples
> 
> #  if(interactive()){
>     library("MotifDb")
See system.file("LICENSE", package="MotifDb") for use restrictions.
>     matrix.fly <- query(MotifDb, "Dmelanogaster")
>     motifs <- as.list(matrix.fly)
>     motifs <- motifs[grepl("Dmelanogaster-FlyFactorSurvey-", names(motifs), fixed=TRUE)]
>     names(motifs) <- gsub("Dmelanogaster_FlyFactorSurvey_", "", 
+                 gsub("_FBgn[0-9]+$", "", 
+                   gsub("[^a-zA-Z0-9]","_", 
+                      gsub("(_[0-9]+)+$", "", names(motifs)))))
>     motifs <- motifs[unique(names(motifs))]
>     pfms <- sample(motifs, 50)
>     pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]], name=.ele)},pfms)
>     motifStack(pfms, "radialPhylog")
> #  }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>