motifStack: plot a DNA sequence logo stack

Description Usage Arguments Value Examples

View source: R/motifStack.R

Description

Plot a DNA sequence logo stack

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
  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")
  }

motifStack documentation built on May 2, 2018, 3:40 a.m.