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, 0.5),
      rot.per = 0.1,
      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() || 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)})
        motifSig <- motifSignature(pfms, phylog, cutoffPval=0.0001)
        motifCloud(motifSig)
      }

[Package motifStack version 1.36.1 Index]