browseMotifs: browse motifs

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

Description

browse motifs in a web browser

Usage

browseMotifs(
  pfms,
  phylog,
  layout = c("tree", "cluster", "radialPhylog"),
  nodeRadius = 2.5,
  baseWidth = 12,
  baseHeight = 30,
  xaxis = TRUE,
  yaxis = TRUE,
  width = NULL,
  height = NULL,
  ...
)

Arguments

pfms	a list of pfm
phylog	layout type. see GraphvizLayouts
layout	layout type. Could be tree, cluster or radialPhylog.
nodeRadius	node radius, default 2.5px.
baseWidth, baseHeight	width and height of each alphabet of the motif logo.
xaxis, yaxis	plot x-axis or y-axis or not in the motifs.
width	width of the figure
height	height of the figure
...	parameters not used

Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

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, 10)
 pfms <- mapply(pfms, names(pfms), FUN=function(.ele, .name){
                  new("pfm",mat=.ele, name=.name)})
 browseMotifs(pfms)
}

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