motifCloud {motifStack} | R Documentation

## plot a DNA sequence logo cloud

### Description

Plot a DNA sequence logo cloud

### Usage

    motifCloud(motifSig, rcpostfix="(RC)",
               layout=c("rectangles", "cloud", "tree"),
               scale=c(6, .5), rot.per=.1,
               draw.box=TRUE, draw.freq=TRUE,
               box.col="gray", freq.col="gray",
               group.col=NULL, groups=NULL, draw.legend=FALSE,
               font="Helvetica-Bold", ic.scale=TRUE)

### Arguments

`motifSig` | an object of class motifSig
`rcpostfix` | postfix for reverse-complement motif names, default: (RC)
`layout` | layout of the logo cloud, rectangles, cloud or tree
`scale` | A vector of length 2 indicating the range of the size of the sequence logo.
`rot.per` | proportion sequence logo with 90 degree rotation. Only work for "cloud" layout
`draw.box` | draw box for each sequence logo or not
`draw.freq` | label frequency of each signature or not
`box.col` | color of box for each sequence logo
`freq.col` | color of frequency label
`group.col` | color setting for groups
`groups` | a named vectors of motif groups
`draw.legend` | draw group color legend or not
`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

### 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)
        motifSig <- motifSignature(pfms, phylog, groupDistance=0.1)
        motifCloud(motifSig)
      }

[Package motifStack version 1.28.0 Index]