motifStack: plot a DNA sequence logo stack

In jianhong/motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

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. And the 'revcomp' parameter for DNAmotifAlignment.

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)
  }

jianhong/motifStack documentation built on Jan. 31, 2024, 5:03 a.m.