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"),
      reorder = TRUE,
      ...
    )

### Arguments

`pfms` | a list of objects of class pfm
`layout` | layout of the logo stack, stack, treeview or radialPhylog
`reorder` | logical(1). Default TRUE. Set to FALSE will do alignment but keep the order of the pfms. This parameter only work for stack layout.
`...` | any parameters could to pass to plotMotifLogoStack, plotMotifLogoStackWithTree, plotMotifStackWithPhylog or plotMotifStackWithRadialPhylog

### Value

return a list contains pfms and phylog

### Examples

      if(interactive() || Sys.getenv("USER")=="jianhongou"){
        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 <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                     new("pfm",mat=.ele, name=.name)})
        motifStack(pfms, "radialPhylog")

        ## AA motifs
        pcms<-importMatrix(system.file("extdata", "prot.meme",
                                       package="motifStack"),
                       format="meme", to="pfm")
        motifStack(pcms[1:5])
        motifStack(pcms[1:5], reorder=FALSE)
      }

[Package motifStack version 1.38.0 Index]