motifStack {motifStack} | R Documentation |
Plot a DNA sequence logo stack
motifStack(pfms, layout=c("stack", "treeview", "phylog", "radialPhylog"), ...)
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 |
return a list contains pfms and phylog
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") }