motifStack (version 1.16.2)

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

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, fontsize=12)

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

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.

fontsize

font size of the template for grImport, default 12. Higher value make better quality figure, but also increase the file size.

Value

• none

See Also

plot.phylog

Examples

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)
    jaspar.scores <- MotIV::readDBScores(file.path(find.package("MotIV"), 
                                    "extdata", "jaspar2010_PCC_SWU.scores"))
    d <- MotIV::motifDistances(lapply(pfms, pfm2pwm))
    hc <- MotIV::motifHclust(d, method="average")
    phylog <- hclust2phylog(hc)
    leaves <- names(phylog$leaves)
    pfms <- pfms[leaves]
    pfms <- lapply(names(pfms), function(.ele, pfms){new("pfm",mat=pfms[[.ele]], 
                                                     name=.ele)},pfms)
    pfms <- DNAmotifAlignment(pfms, minimalConsensus=3)
    plotMotifStackWithPhylog(phylog, pfms, f.phylog=0.3, 
                             cleaves = 0.5, clabel.leaves = 0.7)
  }