plotMotifStackWithPhylog {motifStack} | R Documentation

## 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)

### 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()){
        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)
      }

[Package motifStack version 1.28.0 Index]