plotMotifStackWithPhylog: plot sequence logo stacks with a ape4-style phylogenic tree

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

Description

plot sequence logo stacks with a ape4-style phylogenic tree

Usage

plotMotifStackWithPhylog(
  phylog,
  pfms = NULL,
  f.phylog = 0.3,
  f.logo = NULL,
  cleaves = 1,
  cnodes = 0,
  labels.leaves = names(phylog$leaves),
  clabel.leaves = 1,
  labels.nodes = names(phylog$nodes),
  clabel.nodes = 0,
  font = "Helvetica-Bold",
  ic.scale = TRUE
)

Arguments

phylog	an object of class phylog
pfms	a list of objects of class pfm
f.phylog	a size coefficient for tree size (a parameter to draw the tree in proportion to leaves label)
f.logo	a size coefficient for the motif
cleaves	a character size for plotting the points that represent the leaves, used with par("cex")*cleaves. If zero, no points are drawn
cnodes	a character size for plotting the points that represent the nodes, used with par("cex")*cnodes. If zero, no points are drawn
labels.leaves	a vector of strings of characters for the leaves labels
clabel.leaves	a character size for the leaves labels, used with par("cex")*clavel.leaves
labels.nodes	a vector of strings of characters for the nodes labels
clabel.nodes	a character size for the nodes labels, used with par("cex")*clabel.nodes. If zero, no nodes labels are drawn
font	font of logo
ic.scale	logical If TRUE, the height of each column is proportional to its information content. Otherwise, all columns have the same height.

Value

none

See Also

plot.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)
    hc <- clusterMotifs(pfms)
    library(ade4)
    phylog <- ade4::hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                 new("pfm",mat=.ele, name=.name)})
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    plotMotifStackWithPhylog(phylog, pfms, f.phylog=0.3, 
                             cleaves = 0.5, clabel.leaves = 0.7)
  }

motifStack documentation built on Nov. 8, 2020, 7:43 p.m.