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 1.37.6 Index]