motifCloud: plot a DNA sequence logo cloud

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

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)
  }

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