motifStack {motifStack} | R Documentation

## plot a DNA sequence logo stack

### Description

Plot a DNA sequence logo stack

### Usage

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

### Arguments

`pfms` | a list of objects of class pfm
`layout` | layout of the logo stack, stack, treeview or radialPhylog
`...` | any parameters could to pass to plotMotifLogoStack, plotMotifLogoStackWithTree, plotMotifStackWithPhylog or plotMotifStackWithRadialPhylog

### 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")
      }

[Package motifStack version 1.32.1 Index]